Selective hdac6 inhibitors

ABSTRACT

The present invention provides a compound having the structure: 
     
       
         
         
             
             
         
       
         
         
           
             wherein 
             R 1  is halogen, —NR 5 R 6 , —NR 5 —C(═O)—R 6 , —NH—C(═O)—OR 7 , —OR 7 , —NO 2 , —CN, —SR 7 , —SO 2 R 7 , —CO 2 R 7 , CF 3 , —SOR 7 , —POR 7 , —C(═S)R 7 , —C(═O)—NR 5 R 6 , —CH 2 —C(═O)—NR 5 R 6 , —C(═NR 5 )R 6 , —P(═O)(OR 5 )(OR 6 ), —P(OR 5 )(OR 6 ), —C(═S)R 7 , C 1-5  alkyl, C 2-5  alkenyl, C 2-5  alkynyl, aryl, heteroaryl, or heterocyclyl,
           wherein R 5 , R 6 , and R 7  and are each, independently, H, C 1-5  alkyl, C 2-5  alkenyl, C 2-5  alkynyl, heteroalkyl, hydroxyalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, C 1-5  alkyl-aryl, or C 1-5  alkyl-NH-aryl;   
         
             Ar 1  is phenyl or thiophene; 
             wherein when Ar 1  is phenyl, then R 1  is other than —C(═O)—NR 5 R 6 , where one of R 5  or R 6  is phenyl or quinoline and the other of R 5  or R 6  is hydroxyalkyl, or where one of R 5  or R 6  is quinoline and the other of R 5  or R 6  is H; and 
             wherein when Ar 1  is phenyl, then R 1  is other than —NR 5 —C(═O)—R 6 , where one of R 5  is H and R 6  is quinoline,
 
or a pharmaceutically acceptable salt thereof.

This application claims priority of U.S. Provisional Application No.61/920,307, filed Dec. 23, 2013, the contents of which are herebyincorporated by reference.

Throughout this application, certain publications are referenced inparentheses. Full citations for these publications may be foundimmediately preceding the claims. The disclosures of these publicationsin their entireties are hereby incorporated by reference into thisapplication in order to describe more fully the state of the art towhich this invention relates.

BACKGROUND OF THE INVENTION

To date, eighteen histone deacetylases (HDACs) have been identified inhumans. Eleven HDACs (HDAC1-11) are zinc-dependent and seven HDACs,designated sirtuins 1-7, are NAD⁺-dependent (Parmigiani, R. B. et al.2008). Aberrant activity of HDACs has been implicated in many diseasestates, including cancer (Butler, K. V. et al. 2008). Whenzinc-dependent HDACs are inhibited, the levels of acetylation of certainproteins are elevated, with many resulting physiological effects. Manyinhibitors of HDACs have been developed for use against cancers andother disease states. One well-known HDAC inhibitor, suberoylanilidehydroxamic acid (SAHA, Vorinostat), was approved in 2006 for human usefollowing the results of more than 100 human trials against variousforms of cancer and is currently in use. Phase I, II and III clinicaltrials with vorinostat as single therapy and in combination therapy withvarious anti-cancer agents for hematologic and solid neoplasms areongoing.

While HDACs are associated with deacetylation of histones in the contextof gene expression and chromatin remodeling, there is abundant evidenceindicating that not all functions of HDACs are dedicated todeacetylation of histones. Rather, some HDACs have been shown to exertdeacetylase activity on proteins other than histones. One such HDAC isHDAC6, a cytoplasmic, microtubule-associated deacetylase, which has beenfound to regulate microtubule acetylation and chemotactic cell motility(Kawaguchi, Y. et al. 2003).

HDAC6 is predominantly a cytoplasmic, microtubule-associated member ofthe class IIB family of histone deacetylases. HDAC6 possesses twocatalytic domains, a ubiquitin-binding domain and a C-terminal zincfinger domain (Bali, P. et al. 2005). HDAC6 catalyzes deacetylation ofcytoplasmic protein substrates, such as α-tubulin, Hsp90,peroxiredoxins, and cortactin (Bali, P. et al. 2005). HDAC6 has alsobeen demonstrated to direct misfolded protein aggregates intoaggresomes, which are major repositories formed to manage excessivelevels of misfolded and aggregated protein for eventual elimination.Aggresomes are of clinical interest as they are similar to cytoplasmicinclusion bodies commonly observed in neurodegenerative diseases (Gao,Y.-S. et al. 2010).

It has been shown that the C-terminal catalytic domain of HDAC6, thedomain responsible for α-tubulin deacetylation, can be inhibited by thesmall-molecule inhibitor, tubacin (Haggarty, S. J. et al. 2003).Haggarty et al found that the inhibition of HDAC6 with tubacin did notaffect the stability of microtubules, but decreased cell motility. Giventhe dependence of metastasis and angiogenesis on cell movement,increasing the acetylation level of α-tubulin may be an importantcomponent to the antimetastatic and antiangiogenic activities of HDACinhibitors (Haggarty, S. J. et al. 2003).

Heat shock protein 90 (Hsp90) is an important chaperone protein involvedin protein folding and is overexpressed in many cancer cell types(Butler, K. V. et al. 2008; Kovacs, J. J. et al. 2005). The disruptionof the folding and chaperoning functions of Hsp90 causes its clientproteins to be destabilized and eventually degraded. HDAC6 is anattractive target for cancer treatment because acetylated Hsp90 has areduced ability to perform its chaperoning function (Butler, K. V. etal. 2008; Kovacs, J. J. et al. 2005), with consequent activation of theintrinsic pathway of apoptosis.

In general, for diseases caused by aberrant gene transcription, the mosteffective treatment would involve targeting only the genes relevant tothe disease (Butler, K. V. et al. 2008). In the context of HDACinhibitor treatment, this would involve inhibiting only those HDACisoforms relevant to the disease state, thereby minimizing changes notrelated to the disease, and possibly reducing side effects and toxicity.While SAHA combines efficacy with minimum toxicity, its inhibitoryactivity is not selective among the known human HDACs.

Marks & Breslow (Marks, P. et al. 2007; Marks, P. et al. 2010) describesthe development of HDAC inhibitor voronistat as an anti-cancer drug.HDAC inhibitors have also been identified as a correction forcholesterol and sphingolipid transport defects in human Niemann-Picktype C disease (Munkacsi, A. B. et al. 2011).

In view of the importance of inhibiting only those HDAC isoformsrelevant to a disease state, minimizing acetylation of proteins notrelated to the disease, and reducing side effects and toxicity, new HDACinhibitors that are selective for specific HDACs are needed.

SUMMARY OF THE INVENTION

The present invention provides a compound having the structure:

-   -   wherein    -   R₁ is halogen, —NR₅R₆, —NR₅—C(═O)—R₆, —NH—C(═O)—OR₇, —OR₇, —NO₂,        —CN, —SR₇, —SO₂R₇, —CO₂R₇, CF₃, —SOR₇, —POR₇, —C(═S)R₇,        —C(═O)—NR₅R₆, —CH₂—C(═O)—NR₅R₆, —C(═NR₅)R₆, —P(═O)(OR₅)(OR₆),        —P(OR₅)(OR₆), —C(═S)R₇, C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl,        aryl, heteroaryl, or heterocyclyl,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl,            hydroxyalkyl, cycloalkyl, heterocycloalkyl, aryl,            heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅ alkyl-NH-aryl;    -   Ar₁ is phenyl or thiophene;    -   wherein when Ar₁ is phenyl, then R₁ is other than —C(═O)—NR₅R₆,        where one of R₅ or R₆ is phenyl or quinoline and the other of R₅        or R₆ is —CH₂CH₂OH, or where one of R₅ or R₆ is quinoline and        the other of R₅ or R₆ is H; and    -   wherein when Ar₁ is phenyl, then R₁ is other than —NR₅—C(═O)—R₆,        where R₅ is H and R₆ is quinoline,        or a pharmaceutically acceptable salt thereof.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Schematic representation of HDAC6.

FIG. 2. Blot showing accumulation of acetylated alpha-tubulin andacetylated histone H3 in LNCaP (human prostate cancer cells) culturedwith compounds 8 or 11. GADPH used as loading control.

FIG. 3. Cell growth of HFS (normal) and LNCaP (transformed) cellstreated with compound 8 over 72 h.

FIG. 4. Cell viability of HFS (normal) and LNCaP (transformed) cellstreated with compound 8 over 72 h.

FIG. 5. Western blots of acetylated alpha-tubulin (Acet-Tub) andacetylated histone H3 (Acet-H3) in HFS (normal) and LNCaP (transformed)cells treated with compound 8 at 8, 16, 32, and 64 μM for 24 h. Westernblots of GAPDH and total histone H3 (Total-H3) are loading controls.

FIG. 6. Average weight of immune-deficient mice treated daily by 30 μLintraperitoneal injection with indicated doses of compound 8. DMSO isthe vehicle control.

FIG. 7. Immunoblots of spleens harvested at indicated times after thelast injection. Immune-deficient mice were treated daily by 30 μLintraperitoneal injection with indicated doses of compound 8. DMSO isthe vehicle control. Western blots of acetylated alpha-tubulin(Acet-Tub) and acetylated histone H3 (Acet-H3). Western blots of HSP90and total histone H3 (Total-H3) are loading controls.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a compound having the structure:

-   -   wherein    -   R₁ is halogen, —NR₅R₆, —NR₅—C(═O)—R₆, —NH—C(═O)—OR₇, —OR₇, —NO₂,        —CN, —SR₇, —SO₂R₇, —CO₂R₇, CF₃, —SOR₇, —POR₇, —C(═S)R₇,        —C(═O)—NR₅R₆, —CH₂—C(═O)—NR₅R₆, —C(═NR₅)R₆, —P(═O)(OR₅)(OR₆),        —P(OR₅)(OR₆), —C(═S)R₇, C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl,        aryl, heteroaryl, or heterocyclyl,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl,            hydroxyalkyl, cycloalkyl, heterocycloalkyl, aryl,            heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅ alkyl-NH-aryl;    -   Ar₁ is phenyl or thiophene;    -   wherein when Ar₁ is phenyl, then R₁ is other than —C(═O)—NR₅R₆,        where one of R₅ or R₆ is phenyl or quinoline and the other of R₅        or R₆ is —CH₂CH₂OH, or where one of R₅ or R₆ is quinoline and        the other of R₅ or R₆ is H; and    -   wherein when Ar₁ is phenyl, then R₁ is other than —NR₅—C(═O)—R₆,        where R₅ is H and R₆ is quinoline,        or a pharmaceutically acceptable salt thereof.

In some embodiments, the compound wherein

-   -   Ar₁ is

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, C₂₋₅ alkenyl, C₂₋₇ alkynyl, heteroalkyl,            hydroxyalkyl, cycloalkyl, heterocycloalkyl, aryl,            heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅ alkyl-NH-aryl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, hydroxyalkyl, aryl, heteroaryl, C₁₋₅ alkyl-aryl, or            C_(1-s) alkyl-NH-aryl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein        -   R₅ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl;        -   R₆ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl; and        -   R₇ is C₁₋₅ alkyl, hydroxyalkyl, aryl, heteroaryl, or C₁₋₅            alkyl-NH-aryl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently, phenyl,            —CH₂CH₂OH, —CH₂-phenyl, or —CH₂CH₂N(H)-phenyl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently,

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆,        -   wherein R₅ is

In some embodiments, the compound wherein

-   -   R₁ is —NR₅—C(═O)—R₆,        -   wherein R₅ is

In some embodiments, the compound wherein

-   -   R₁ is —CO₂R₇,        -   wherein R₇

The present invention provides a compound having the structure:

-   -   wherein    -   R₁ is halogen, —NR₅R₆, —NR₅—C(═O)—R₆, —NH—C(═O)—OR₇, —OR₇, —NO₂,        —CN, —SR₇, —SO₂R₇, —CO₂R₇, CF₃, —SOR₇, —POR₇, —C(═S)R₇,        —C(═O)—NR₅R₆, —CH₂—C(═O)—NR₅R₆, —C(═NR₅)R₆, —P(═O)(OR₅)(OR₆),        —P(OR₅)(OR₆), —C(═S)R₇, C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl,        aryl, heteroaryl, or heterocyclyl,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl,            hydroxyalkyl, cycloalkyl, heterocycloalkyl, aryl,            heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅ alkyl-NH-aryl;    -   wherein R₁ is other than —C(═O)—NR₅R₆, where one of R₅ or R₆ is        phenyl or quinoline and the other of R₅ or R₆ is —CH₂CH₂OH, or        where one of R₅ or R₆ is quinoline and the other of R₅ or R₆ is        H; and    -   wherein R₁ is other than —NR₅—C(═O)—R₅ where R₅ is H and R₆ is        quinoline,        or a pharmaceutically acceptable salt thereof.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl,            hydroxyalkyl, cycloalkyl, heterocycloalkyl, aryl,            heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅ alkyl-NH-aryl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, hydroxyalkyl, aryl, heteroaryl, C₁₋₅ alkyl-aryl, or            C₁₋₅ alkyl-NH-aryl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇        -   wherein        -   R₅ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl;        -   R₆ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl; and        -   R₇ is C₁₋₅ alkyl, hydroxyalkyl, aryl, heteroaryl, or C₁₋₅            alkyl-NH-aryl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently, phenyl,            —CH₂CH₂OH, —CH₂-phenyl, or —CH₂CH₂N(H)-phenyl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently,

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆,        -   wherein R₅ is

In some embodiments, the compound wherein

-   -   R₁ is —NR₅—C(═O)—R₆,        -   wherein R₅ is

In some embodiments, the compound wherein

-   -   R₁ is —CO₂R₇,        -   wherein R₇

The present invention provides a compound having the structure:

-   -   wherein    -   R₁ is halogen, —NR₅R₆, —NR₅—C(═O)—R₆, —NH—C(═O)—OR₇, —OR₇, —NO₂,        —CN, —SR₇, —SOR₇, —CO₂R₇, CF₃, —SOR₇, —POR₇, —C(═S)R₇,        —C(═O)—NR₅R₆, —CH₂—C(═O)—NR₅R₆, —C(═NR₅)R₆, —P(═O)(OR₅)(OR₆),        —P(OR₅)(OR₆), —C(═S)R₇, C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl,        aryl, heteroaryl, or heterocyclyl,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl,            hydroxyalkyl, cycloalkyl, heterocycloalkyl, aryl,            heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅ alkyl-NH-aryl,            or a pharmaceutically acceptable salt thereof.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl,            hydroxyalkyl, cycloalkyl, heterocycloalkyl, aryl,            heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅ alkyl-NH-aryl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅            alkyl, hydroxyalkyl, aryl, heteroaryl, C₁₋₅ alkyl-aryl, or            C₁₋₅ alkyl-NH-aryl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇        -   wherein        -   R₅ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl;        -   R₆ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl; and        -   R₇ is C₁₋₅ alkyl, hydroxyalkyl, aryl, heteroaryl, or C₁₋₅            alkyl-NH-aryl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently, phenyl,            —CH₂CH₂OH, —CH₂-phenyl, or —CH₂CH₂N(H)-phenyl.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein R₅, R₆, and R₇ and are each, independently,

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆,        -   wherein R₅ is

In some embodiments, the compound wherein

-   -   R₁ is —NR₅—C(═O)—R₆,        -   wherein R₅ is

In some embodiments, the compound wherein

-   -   R₁ is —CO₂R₇,        -   wherein R₇

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein        -   R₅ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl;        -   R₆ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl; and        -   R₇ is C₁₋₅ alkyl, hydroxyalkyl, aryl, heteroaryl, or C₁₋₅            alkyl-NH-aryl; and    -   Ar₁ is phenyl or thiophene,        or a pharmaceutically acceptable salt thereof.

In some embodiments, the compound wherein

-   -   R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇,        -   wherein        -   R₅ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl;        -   R₆ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl; and        -   R₇ is C₁₋₅ alkyl, hydroxyalkyl, aryl, heteroaryl, or C₁₋₅            alkyl-NH-aryl; and    -   Ar₁ is

or a pharmaceutically acceptable salt thereof.

In some embodiments, the compound having the structure:

or a pharmaceutically acceptable salt thereof.

In some embodiments, the compound having the structure:

or a pharmaceutically acceptable salt thereof.

The present invention provides pharmaceutical composition comprising thecompound of the present invention and a pharmaceutically acceptablecarrier.

The present invention provides a method of inhibiting the activity of ahistone deacetylase in a cell comprising contacting the histonedeacetylase with the compound of the present invention so as to inhibitthe activity of the histone deacetylase. In some embodiments, thehistone deacetylase is HDAC6.

The present invention provides a method of inhibiting the activity of ahistone deacetylase 6 (HDAC6) in a cell comprising contacting thehistone deacetylase 6 with the compound of the present invention so asto inhibit the activity of the histone deacetylase 6 in the cell. Thepresent invention provides a method of increasing accumulation ofacetylated alpha-tubulin in a cell comprising contacting the cell withthe compound of the present invention so as to increase the accumulationof acetylated alpha-tubulin in the cell.

The present invention provides a method of treating a neurodegenerativedisease in a subject comprising administering an effective amount of thecompound of the present invention to the subject so as to treat theneurodegenerative disease in the subject.

In some embodiments, the method wherein the neurodegenerative disease isParkinson's disease, Alzheimer's disease, Huntington's disease orNiemann-Pick type C disease.

The present invention provides a method of treating a disease associatedwith defective lipid transport in a subject comprising administering aneffective amount of the compound of the present invention to the subjectso as to treat the disease in the subject.

In some embodiments, the method wherein the disease associated withdefective lipid transport is Stargardt disease, macular degeneration,Harlequin ichthyosis or Tangier disease.

The present invention provides a method of treating cancer in a subjectcomprising administering an effective amount of the compound of thepresent invention to the subject so as to treat the cancer in thesubject.

The present invention provides a method of treating HIV infection in asubject comprising administering an effective amount of the compound ofthe present invention to the subject so as to treat the HIV infection inthe subject.

The present invention provides a method of treating latent HIV infectionin a subject comprising administering an effective amount of thecompound of the present invention to the subject so as to treat thelatent HIV infection in the subject.

The present invention provides a method of enhancing the anti-canceractivity of an anti-cancer agent in a subject afflicted with a cancer,comprising administering to the subject the compound of the presentinvention in an amount effective to enhance the anti-cancer activity ofthe anti-cancer agent.

The present invention provides a method of treating a subject afflictedwith cancer comprising periodically administering to the subject a) anamount of the compound of the present invention or a pharmaceuticallyacceptable salt thereof, and b) an anti-cancer agent, wherein theamounts when taken together are more effective to treat the subject thanwhen each agent at the same amount is administered alone.

In some embodiments, the method wherein the anti-cancer agent is SAHA,etoposide or paclitaxel.

In some embodiments, the method wherein the anti-cancer agent isselected from x-radiation, ionizing radiation, a DNA damaging agent, aDNA intercalating agent, a microtubule stabilizing agent, a microtubuledestabilizing agent, a spindle toxin, abarelix, aldesleukin,alemtuzumab, alitertinoin, allopurinol, altretamine, amifostin,anakinra, anastrozole, arsenic trioxide, asparaginase, azacitidine,bevacizumab, bexarotene, bleomycin, bortezomib, busulfan, calusterone,capecitabine, carboplatin, carmustine, celecoxib, cetuximab,chlorambucil, cisplatin, cladribine, clofarabine, cyclophosphamide,cytarabine, dacarbazine, dactinomycin, actinomycin D, dalteparin sodium,darbepoetin alfa, dasatinib, daunorubicin, daunomycin, decitabine,denileukin, dexrazoxane, docetaxel, doxorubicin, dromostanolonepropionate, exulizumab, epirubicin, epoetin alfa, erlotinib,estramustine, etoposide phosphate, etoposide, VP-16, exemestane,fentanyl citrate, filgrastim, floxuridine, fludarabine, fluorouracil,fulvestrant, gefitinib, gemcitabine, gosereline acetate, histrelinacetate, hydroxyurea, ibritumomab tiuxetan, idarubicin, ifosfamide,imatinib mesylate, interferon alfa 2a, interferon alfa 2b, irinotecan,lapatinib ditosylate, lenalidomide, letrozole, leucovrin, leuprolideacetate, levamisole, lomustine, meclorethamine, megestrol acetate,melphalan, mercaptopurine, mesna, methotrexate, methoxsalen, mitomycinC, mitotane, mitoxantrone, nandrolone phenpropionate, nelarabine,nofetumomab, oprelvekin, oxaliplatin, paclitaxel, palifermin,pamidronate, panitumumab, pegademase, pegaspargase, pegfilgrastim,peginterferon alfa 2b, pemetrexed disodium, pentostatin, pipobroman,plicamycin, mithramycin, porfimer sodium, procarbazine, quinacrine,rasburicase, rituximab, SAHA, sargrmostim, sorafenib, streptozocin,sunitinib, sunitinib maleate, talc, tamoxifen, temozolomide, teniposide,VM-26, testolactone, thalidomide, thioguanine, G-TG, thiotepa,topotecan, toremifene, tositumomab, trastuzumab, tretinoin ATRA, uracilmustard, valrunicin, vinblastine, vincristine, vinorelbine, vorinostat,zoledronate, zoledronic acid, abraxane or brentuximab vedotin.

In some embodiments, a pharmaceutical composition comprising thecompound of the present invention or a pharmaceutically acceptable saltthereof and an anti-cancer agent, and at least one pharmaceuticallyacceptable carrier.

In some embodiments, the use of the compound of the present invention ora pharmaceutically acceptable salt thereof and an anti-cancer agent inthe preparation of a combination for treating a subject afflicted withcancer wherein the amount of the compound and the amount of theanti-cancer agent are administered simultaneously or contemporaneously.

In some embodiments, a pharmaceutical composition comprising an amountof the compound of the present invention or a pharmaceuticallyacceptable salt thereof for use in treating a subject afflicted withcancer as an add-on therapy or in combination with, or simultaneously,contemporaneously or concomitantly with an anti-cancer agent.

In some embodiments, the compound of the present invention or apharmaceutically acceptable salt thereof for use as an add-on therapy orin combination with an anti-cancer agent in treating a subject afflictedwith cancer.

In some embodiments, the compound of the present invention or apharmaceutically acceptable salt thereof and an anti-cancer agent forthe treatment of a subject afflicted with cancer wherein the compoundand the anti-cancer agent are administered simultaneously, separately orsequentially.

In some embodiments, the subject is a human.

In some embodiments, a product containing an amount of the compound ofthe present invention or a pharmaceutically acceptable salt thereof andan amount of an anti-cancer agent for simultaneous, separate orsequential use in treating a subject afflicted cancer.

In some embodiments, the compound of the present invention or apharmaceutically acceptable salt thereof in combination with ananti-cancer agent for use in treating cancer.

In some embodiments, a pharmaceutical composition comprising thecompound of the present invention and a pharmaceutically acceptablecarrier.

In some embodiments, a method of inhibiting the activity of a histonedeacetylase in a cell comprising contacting the histone deacetylase withthe compound or composition of the present invention so as to inhibitthe activity of the histone deacetylase.

In some embodiments, a method of inhibiting the activity of a histonedeacetylase, wherein the histone deacetylase is HDAC6.

In some embodiments, a method of inhibiting the activity of a histonedeacetylase 6 (HDAC6) in a cell comprising contacting the histonedeacetylase 6 with the compound or composition of the present inventionso as to inhibit the activity of the histone deacetylase 6 in the cell.

In some embodiments, a method of increasing accumulation of acetylatedalpha-tubulin in a cell comprising contacting the cell with any one ofthe compound or composition of the present invention so as to increasethe accumulation of acetylated alpha-tubulin in the cell.

In some embodiments, a method of treating a neurodegenerative disease ina subject comprising administering an effective amount of the compoundor composition of the present invention to the subject so as to treatthe neurodegenerative disease in the subject.

In some embodiments, a method of treating a neurodegenerative diseasewherein the neurodegenerative disease is Parkinson's disease,Alzheimer's disease, Huntington's disease or Niemann-Pick type Cdisease.

In some embodiments, a method of treating a disease associated withdefective lipid transport in a subject comprising administering aneffective amount of the compound or composition of the present inventionto the subject so as to treat the disease in the subject.

In some embodiments, a method of treating a disease associated withdefective lipid transport wherein the disease associated with defectivelipid transport is Stargardt disease, macular degeneration, Harlequinichthyosis or Tangier disease.

A method of inhibiting the activity of a histone deacetylase in a cellcomprising contacting the histone deacetylase with any one, or more, ofthe instant compounds so as to inhibit the activity of the histonedeacetylase. In an embodiment the histone deacetylase is HDAC6.

A method of inhibiting the activity of a histone deacetylase 6 (HDAC6)in a cell comprising contacting the histone deacetylase 6 with any one,or more, of the instant compounds so as to inhibit the activity of thehistone deacetylase 6 in the cell.

A method of increasing accumulation of acetylated alpha tubulin in acell comprising contacting the cell with any one, or more, of theinstant compounds so as to increase the accumulation of acetylatedalpha-tubulin in the cell.

In some embodiments, a method for reducing one or more symptoms ofdisease in a subject, comprising administering an effective amount ofthe compound of the present invention or the composition of the presentinvention to the subject so as to treat the disease in the subject.

In some embodiments, a method of treating cancer in a subject comprisingadministering an effective amount of the compound of the presentinvention to the subject so as to treat the cancer in the subject.

In some embodiments, a method for inhibiting the growth of a tumorcomprising contacting the tumor with the compound of the presentinvention or the composition of the present invention. In someembodiments, a method for reducing the size of a tumor comprisingcontacting the tumor with the compound of the present invention or thecomposition of the present invention

In some embodiments, the invention provides a method of reducing one ormore symptoms of any disease that involves carcinomas including but notlimited to lung cancer, breast cancer, prostate cancer, cervical cancer,pancreatic cancer, colon cancer, ovarian cancer; stomach cancer,esophagus cancer, mouth cancer, tongue cancer, gum cancer, skin cancer(e.g., melanoma, basal cell carcinoma, Kaposi's sarcoma, etc.), musclecancer, heart cancer, liver cancer, bronchial cancer, cartilage cancer,bone cancer, testis cancer, kidney cancer, endometrium cancer, uteruscancer, bladder cancer, bone marrow cancer, lymphoma cancer, spleencancer, thymus cancer, thyroid cancer, brain cancer, neuron cancer,mesothelioma, gall bladder cancer, ocular cancer (e.g., cancer of thecornea, cancer of uvea, cancer of the choroids, cancer of the macula,vitreous humor cancer, etc.), joint cancer (such as synovium cancer),glioblastoma, lymphoma, and leukemia. Malignant neoplasms are furtherexemplified by sarcomas (such as osteosarcoma and Kaposi's sarcoma).

In some embodiments, a method of treating HIV infection in a subjectcomprising administering an effective amount of the compound of thepresent invention to the subject so as to treat the HIV infection in thesubject.

In some embodiments, a method of treating latent HIV infection in asubject comprising administering an effective amount of the compound ofthe present invention to the subject so as to treat the latent HIVinfection in the subject.

In some embodiments, a method wherein the subject is infected with HIV.In some embodiments, the invention provides a method of reducing one ormore symptoms of HIV infection. In some embodiments, a method ofinhibiting HIV replication by contacting an HIV-infected cell with thecompound of the present invention. In some embodiments, the HIV-infectedcells are HIV reservoir cells.

This invention also provides isotopic variants of the compoundsdisclosed herein, including wherein the isotopic atom is ²H and/orwherein the isotopic atom ¹³C. Accordingly, in the compounds providedherein hydrogen can be enriched in the deuterium isotope. It is to beunderstood that the invention encompasses all such isotopic forms whichinhibit HDAC, including those which inhibit HDAC6 selectively overHDAC1.

A method of treating a neurodegenerative disease in a subject comprisingadministering an effective amount of any one, or more, of the instantcompounds to the subject so as to treat the neurodegenerative disease inthe subject.

In an embodiment, the neurodegenerative disease is Parkinson's disease,Alzheimer's disease, Huntington's disease or Niemann-Pick type Cdisease.

A method of treating a disease associated with defective lipid transportin a subject comprising administering an effective amount of any one, ormore, of the instant compounds to the subject so as to treat the diseasein the subject.

In an embodiment, the disease associated with defective lipid transportis Stargardt disease, macular degeneration, Harlequin ichthyosis orTangier disease.

In some embodiments of any one the above methods, uses, pharmaceuticalcompositions, compounds or products, the compound has the structure ofcompound 8, compound 11, compound 23, compound 32, or compound 36.

It is understood that the structures described in the embodiments of themethods can be the same as the structures of the compounds describedhereinabove.

It is understood that where a numerical range is recited herein, thepresent invention contemplates each integer between, and including, theupper and lower limits, unless otherwise stated.

As used herein, the term “activity” refers to the activation,production, expression, synthesis, intercellular effect, and/orpathological or aberrant effect of the referenced molecule, eitherinside and/or outside of a cell. Such molecules include, but are notlimited to, cytokines, enzymes, growth factors, pro-growth factors,active growth factors, and pro-enzymes. Molecules such as cytokines,enzymes, growth factors, pro-growth factors, active growth factors, andpro-enzymes may be produced, expressed, or synthesized within a cellwhere they may exert an effect. Such molecules may also be transportedoutside of the cell to the extracellular matrix where they may induce aneffect on the extracellular matrix or on a neighboring cell. It isunderstood that activation of inactive cytokines, enzymes andpro-enzymes may occur inside and/or outside of a cell and that bothinactive and active forms may be present at any point inside and/oroutside of a cell. It is also understood that cells may possess basallevels of such molecules for normal function and that abnormally high orlow levels of such active molecules may lead to pathological or aberranteffects that may be corrected by pharmacological intervention.

As used herein, the term “histone deacetylase” or “HDAC” refers to anymember of the classes of enzymes capable of cleaving an acetyl group(—C(═O)CH₃) from proteins, which include, but are not limited to,histones and microtubules. A histone deacetylase may be zinc-dependent.Examples of HDACs include, but are not limited to, HDAC1, HDAC2, HDAC3,HDAC4, HDAC5, HDAC6, HDAC7, HDAC8, HDAC9, HDAC10, and HDAC11.

Except where otherwise specified, the structure of a compound of thisinvention includes an asymmetric carbon atom, it is understood that thecompound occurs as a racemate, racemic mixture, and isolated singleenantiomer. All such isomeric forms of these compounds are expresslyincluded in this invention. Except where otherwise specified, eachstereogenic carbon may be of the R or S configuration. It is to beunderstood accordingly that the isomers arising from such asymmetry(e.g., all enantiomers and diastereomers) are included within the scopeof this invention, unless indicated otherwise. Such isomers can beobtained in substantially pure form by classical separation techniquesand by stereochemically controlled synthesis, such as those described in“Enantiomers, Racemates and Resolutions” by J. Jacques, A. Collet and S.Wilen, Pub. John Wiley & Sons, N Y, 1981. For example, the resolutionmay be carried out by preparative chromatography on a chiral column.

The subject invention is also intended to include all isotopes of atomsoccurring on the compounds disclosed herein. Isotopes include thoseatoms having the same atomic number but different mass numbers. By wayof general example and without limitation, isotopes of hydrogen includetritium and deuterium. Isotopes of carbon include C-13 and C-14.

It will be noted that any notation of a carbon in structures throughoutthis application, when used without further notation, are intended torepresent all isotopes of carbon, such as ¹²C, ¹³C, or ¹⁴C. Furthermore,any compounds containing ¹³C or ¹⁴C may specifically have the structureof any of the compounds disclosed herein.

It will also be noted that any notation of a hydrogen in structuresthroughout this application, when used without further notation, areintended to represent all isotopes of hydrogen, such as ¹H, ²H, or 4H.Furthermore, any compounds containing ²H or ³H may specifically have thestructure of any of the compounds disclosed herein.

Isotopically-labeled compounds can generally be prepared by conventionaltechniques known to those skilled in the art using appropriateisotopically-labeled reagents in place of the non-labeled reagentsemployed.

In the compounds used in the method of the present invention, thesubstituents may be substituted or unsubstituted, unless specificallydefined otherwise.

In the compounds used in the method of the present invention, alkyl,heteroalkyl, monocycle, bicycle, aryl, heteroaryl and heterocycle groupscan be further substituted by replacing one or more hydrogen atoms withalternative non-hydrogen groups. These include, but are not limited to,halo, hydroxy, mercapto, amino, carboxy, cyano and carbamoyl.

It is understood that substituents and substitution patterns on thecompounds used in the method of the present invention can be selected byone of ordinary skill in the art to provide compounds that arechemically stable and that can be readily synthesized by techniquesknown in the art from readily available starting materials. If asubstituent is itself substituted with more than one group, it isunderstood that these multiple groups may be on the same carbon or ondifferent carbons, so long as a stable structure results.

In choosing the compounds used in the method of the present invention,one of ordinary skill in the art will recognize that the varioussubstituents, i.e. R₁, R₂, etc. are to be chosen in conformity withwell-known principles of chemical structure connectivity.

As used herein, “alkyl” includes both branched and straight-chainsaturated aliphatic hydrocarbon groups having the specified number ofcarbon atoms and may be unsubstituted or substituted. Thus, C₁-C_(n) asin “C₁-C_(n) alkyl” is defined to include groups having 1, 2, . . . ,n−1 or n carbons in a linear or branched arrangement (e.g. C₁-C₂ alkyl,C₁-C₃ alkyl, C₁-C₄ alkyl, C₁-C₅ alkyl, or C₁-C₆ alkyl) For example,C₁-C₆, as in “C₁-C₆ alkyl” is defined to include groups having 1, 2, 3,4, 5, or 6 carbons in a linear or branched arrangement, and specificallyincludes methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, pentyl,hexyl, and octyl.

As used herein, “alkenyl” refers to a non-aromatic hydrocarbon radical,straight or branched, containing at least 1 carbon to carbon doublebond, and up to the maximum possible number of non-aromaticcarbon-carbon double bonds may be present, and may be unsubstituted orsubstituted. For example, “C₂-C₆ alkenyl” means an alkenyl radicalhaving 2, 3, 4, 5, or 6 carbon atoms, and up to 1, 2, 3, 4, or 5carbon-carbon double bonds respectively. Alkenyl groups include ethenyl,propenyl, butenyl and cyclohexenyl.

The term “alkynyl” refers to a hydrocarbon radical straight or branched,containing at least 1 carbon to carbon triple bond, and up to themaximum possible number of non-aromatic carbon-carbon triple bonds maybe present, and may be unsubstituted or substituted. Thus, “C₂-C₆alkynyl” means an alkynyl radical having 2 or 3 carbon atoms and 1carbon-carbon triple bond, or having 4 or 5 carbon atoms and up to 2carbon-carbon triple bonds, or having 6 carbon atoms and up to 3carbon-carbon triple bonds. Alkynyl groups include ethynyl, propynyl andbutynyl.

“Alkylene”, “alkenylene” and “alkynylene” shall mean, respectively, adivalent alkane, alkene and alkyne radical, respectively. It isunderstood that an alkylene, alkenylene, and alkynylene may be straightor branched. An alkylene, alkenylene, and alkynylene may beunsubstituted or substituted.

As used herein, “aryl” is intended to mean any stable monocyclic,bicyclic or polycyclic carbon ring of up to 10 atoms in each ring,wherein at least one ring is aromatic, and may be unsubstituted orsubstituted. Examples of such aryl elements include phenyl, p-toluenyl(4-methylphenyl), naphthyl, tetrahydro-naphthyl, indanyl, biphenyl,phenanthryl, anthryl or acenaphthyl. In cases where the aryl substituentis bicyclic and one ring is non-aromatic, it is understood thatattachment is via the aromatic ring.

As used herein, the term “polycyclic” refers to unsaturated or partiallyunsaturated multiple fused ring structures, which may be unsubstitutedor substituted.

The term “arylalkyl” refers to alkyl groups as described above whereinone or more bonds to hydrogen contained therein are replaced by a bondto an aryl group as described above. It is understood that an“arylalkyl” group is connected to a core molecule through a bond fromthe alkyl group and that the aryl group acts as a substituent on thealkyl group. Examples of arylalkyl moieties include, but are not limitedto, benzyl (phenylmethyl), p-trifluoromethylbenzyl(4-trifluoromethylphenylmethyl), 1-phenylethyl, 2-phenylethyl,3-phenylpropyl, 2-phenylpropyl and the like.

The term “heteroaryl”, as used herein, represents a stable monocyclic,bicyclic or polycyclic ring of up to 10 atoms in each ring, wherein atleast one ring is aromatic and contains from 1 to 4 heteroatoms selectedfrom the group consisting of O, N and S. Bicyclic aromatic heteroarylgroups include phenyl, pyridine, pyrimidine or pyridizine rings that are(a) fused to a 6-membered aromatic (unsaturated) heterocyclic ringhaving one nitrogen atom; (b) fused to a 5- or 6-membered aromatic(unsaturated) heterocyclic ring having two nitrogen atoms; (c) fused toa 5-membered aromatic (unsaturated) heterocyclic ring having onenitrogen atom together with either one oxygen or one sulfur atom; or (d)fused to a 5-membered aromatic (unsaturated) heterocyclic ring havingone heteroatom selected from O, N or S. Heteroaryl groups within thescope of this definition include but are not limited to:benzoimidazolyl, benzofuranyl, benzofurazanyl, benzopyrazolyl,benzotriazolyl, benzothiophenyl, benzoxazolyl, carbazolyl, carbolinyl,cinnolinyl, furanyl, indolinyl, indolyl, indolazinyl, indazolyl,isobenzofuranyl, isoindolyl, isoquinolyl, isothiazolyl, isoxazolyl,naphthpyridinyl, oxadiazolyl, oxazolyl, oxazoline, isoxazoline,oxetanyl, pyranyl, pyrazinyl, pyrazolyl, pyridazinyl, pyridopyridinyl,pyridazinyl, pyridyl, pyrimidyl, pyrrolyl, quinazolinyl, quinolyl,quinoxalinyl, tetrazolyl, tetrazolopyridyl, thiadiazolyl, thiazolyl,thienyl, triazolyl, azetidinyl, aziridinyl, 1,4-dioxanyl,hexahydroazepinyl, dihydrobenzoimidazolyl, dihydrobenzofuranyl,dihydrobenzothiophenyl, dihydrobenzoxazolyl, dihydrofuranyl,dihydroimidazolyl, dihydroindolyl, dihydroisooxazolyl,dihydroisothiazolyl, dihydrooxadiazolyl, dihydrooxazolyl,dihydropyrazinyl, dihydropyrazolyl, dihydropyridinyl,dihydropyrimidinyl, dihydropyrrolyl, dihydroquinolinyl,dihydrotetrazolyl, dihydrothiadiazolyl, dihydrothiazolyl,dihydrothienyl, dihydrotriazolyl, dihydroazetidinyl,methylenedioxybenzoyl, tetrahydrofuranyl, tetrahydrothienyl, acridinyl,carbazolyl, cinnolinyl, quinoxalinyl, pyrrazolyl, indolyl,benzotriazolyl, benzothiazolyl, benzoxazolyl, isoxazolyl, isothiazolyl,furanyl, thienyl, benzothienyl, benzofuranyl, quinolinyl, isoquinolinyl,oxazolyl, isoxazolyl, indolyl, pyrazinyl, pyridazinyl, pyridinyl,pyrimidinyl, pyrrolyl, tetra-hydroquinoline. In cases where theheteroaryl substituent is bicyclic and one ring is non-aromatic orcontains no heteroatoms, it is understood that attachment is via thearomatic ring or via the heteroatom containing ring, respectively. Ifthe heteroaryl contains nitrogen atoms, it is understood that thecorresponding N-oxides thereof are also encompassed by this definition.

As used herein, “cycloalkyl” includes cyclic rings of alkanes of threeto eight total carbon atoms, or any number within this range (i.e.,cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl orcyclooctyl).

The term “heterocycle”, “heterocyclyl” or “heterocyclic” refers to amono- or poly-cyclic ring system which can be saturated or contains oneor more degrees of unsaturation and contains one or more heteroatoms.Preferred heteroatoms include N, O, and/or S, including N-oxides, sulfuroxides, and dioxides. Preferably the ring is three to ten-membered andis either saturated or has one or more degrees of unsaturation. Theheterocycle may be unsubstituted or substituted, with multiple degreesof substitution being allowed. Such rings may be optionally fused to oneor more of another “heterocyclic” ring(s), heteroaryl ring(s), arylring(s), or cycloalkyl ring(s). Examples of heterocycles include, butare not limited to, tetrahydrofuran, pyran, 1,4-dioxane, 1,3-dioxane,piperidine, piperazine, pyrrolidine, morpholine, thiomorpholine,tetrahydrothiopyran, tetrahydrothiophene, 1,3-oxathiolane, and the like.

As used herein, “heterocycloalkyl” is intended to mean a 5- to10-membered nonaromatic ring containing from 1 to 4 heteroatoms selectedfrom the group consisting of O, N and S, and includes bicyclic groups.“Heterocycloalkyl” therefore includes, but is not limited to thefollowing: imidazolyl, piperazinyl, piperidinyl, pyrrolidinyl,morpholinyl, thiomorpholinyl, tetrahydropyranyl, dihydropiperidinyl,tetrahydrothiophenyl and the like. If the heterocycle contains nitrogen,it is understood that the corresponding N-oxides thereof are alsoencompassed by this definition.

The alkyl, alkenyl, alkynyl, aryl, heteroaryl and heterocyclylsubstituents may be substituted or unsubstituted, unless specificallydefined otherwise.

In the compounds of the present invention, alkyl, alkenyl, alkynyl,aryl, heterocyclyl and heteroaryl groups can be further substituted byreplacing one or more hydrogen atoms with alternative non-hydrogengroups. These include, but are not limited to, halo, hydroxy, mercapto,amino, carboxy, cyano and carbamoyl.

As used herein, the term “halogen” refers to F, Cl, Br, and I.

As used herein, “heteroalkyl” includes both branched and straight-chainsaturated aliphatic hydrocarbon groups having the specified number ofcarbon atoms and at least 1 heteroatom within the chain or branch.

As used herein, “hydroxyalkyl” includes alkyl groups as described abovewherein one or more bonds to hydrogen contained therein are replaced bya bond to an —OH group. In some embodiments, C₁-C₁₂ hydroxyalkyl orC₁-C₆ hydroxyalkyl. C₁-C_(n) as in “C₁-C_(n) alkyl” is defined toinclude groups having 1, 2, . . . , n−1 or n carbons in a linear orbranched arrangement (e.g. C₁-C₂ hydroxyalkyl, C₁-C₃ hydroxyalkyl, C₁-C₄hydroxyalkyl, C₁-C₅ hydroxyalkyl, or C₁-C₆ hydroxyalkyl) For example,C₁-C₆, as in “C₁-C₆ hydroxyalkyl” is defined to include groups having 1,2, 3, 4, 5, or 6 carbons in a linear or branched alkyl arrangementwherein a hydrogen contained therein is replaced by a bond to an —OHgroup.

As used herein, “monocycle” includes any stable polyatomic carbon ringof up to 10 atoms and may be unsubstituted or substituted. Examples ofsuch non-aromatic monocycle elements include but are not limited to:cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl. Examples of sucharomatic monocycle elements include but are not limited to: phenyl.

As used herein, “bicycle” includes any stable polyatomic carbon ring ofup to 10 atoms that is fused to a polyatomic carbon ring of up to 10atoms with each ring being independently unsubstituted or substituted.Examples of such non-aromatic bicycle elements include but are notlimited to: decahydronaphthalene. Examples of such aromatic bicycleelements include but are not limited to: naphthalene.

The term “alkylaryl” refers to alkyl groups as described above whereinone or more bonds to hydrogen contained therein are replaced by a bondto an aryl group as described above. It is understood that an“alkylaryl” group is connected to a core molecule through a bond fromthe alkyl group and that the aryl group acts as a substituent on thealkyl group. Examples of arylalkyl moieties include, but are not limitedto, benzyl (phenylmethyl), p-trifluoromethylbenzyl(4-trifluoromethylphenylmethyl), 1-phenylethyl, 2-phenylethyl,3-phenylpropyl, 2-phenylpropyl and the like.

The term “ester” is intended to a mean an organic compound containingthe R—O—CO—R′ group.

The term “amide” is intended to a mean an organic compound containingthe R—CO—NH—R′ or R—CO—N—R′R″ group.

The term “phenyl” is intended to mean an aromatic six membered ringcontaining six carbons.

The term “thiophene” is intended to mean a heteroaryl having afive-membered ring containing four carbon atoms and one sulfur atom.

The term “quinoline” is intended to mean a fully aromatic heteroarylhaving a six-membered ring fused to a six-membered ring containing ninecarbon atoms and one nitrogen atom.

The term “substitution”, “substituted” and “substituent” refers to afunctional group as described above in which one or more bonds to ahydrogen atom contained therein are replaced by a bond to non-hydrogenor non-carbon atoms, provided that normal valencies are maintained andthat the substitution results in a stable compound. Substituted groupsalso include groups in which one or more bonds to a carbon(s) orhydrogen(s) atom are replaced by one or more bonds, including double ortriple bonds, to a heteroatom. Examples of substituent groups includethe functional groups described above, and halogens (i.e., F, Cl, Br,and I); alkyl groups, such as methyl, ethyl, n-propyl, isopropryl,n-butyl, tert-butyl, and trifluoromethyl; hydroxyl; alkoxy groups, suchas methoxy, ethoxy, n-propoxy, and isopropoxy; aryloxy groups, such asphenoxy; arylalkyloxy, such as benzyloxy (phenylmethoxy) andp-trifluoromethylbenzyloxy (4-trifluoromethylphenylmethoxy);heteroaryloxy groups; sulfonyl groups, such as trifluoromethanesulfonyl,methanesulfonyl, and p-toluenesulfonyl; nitro, nitrosyl; mercapto;sulfanyl groups, such as methylsulfanyl, ethylsulfanyl andpropylsulfanyl; cyano; amino groups, such as amino, methylamino,dimethylamino, ethylamino, and diethylamino; and carboxyl. Wheremultiple substituent moieties are disclosed or claimed, the substitutedcompound can be independently substituted by one or more of thedisclosed or claimed substituent moieties, singly or plurally. Byindependently substituted, it is meant that the (two or more)substituents can be the same or different.

It is understood that substituents and substitution patterns on thecompounds of the instant invention can be selected by one of ordinaryskill in the art to provide compounds that are chemically stable andthat can be readily synthesized by techniques known in the art, as wellas those methods set forth below, from readily available startingmaterials. If a substituent is itself substituted with more than onegroup, it is understood that these multiple groups may be on the samecarbon or on different carbons, so long as a stable structure results.

In choosing the compounds of the present invention, one of ordinaryskill in the art will recognize that the various substituents, i.e. R₁,R₂, etc. are to be chosen in conformity with well-known principles ofchemical structure connectivity.

The various R groups attached to the aromatic rings of the compoundsdisclosed herein may be added to the rings by standard procedures, forexample those set forth in Advanced Organic Chemistry: Part B: Reactionand Synthesis, Francis Carey and Richard Sundberg, (Springer) 5th ed.Edition. (2007), the content of which is hereby incorporated byreference.

The compounds used in the method of the present invention may beprepared by techniques well know in organic synthesis and familiar to apractitioner ordinarily skilled in the art. However, these may not bethe only means by which to synthesize or obtain the desired compounds.

The compounds used in the method of the present invention may beprepared by techniques described in Vogel's Textbook of PracticalOrganic Chemistry, A. I. Vogel, A. R. Tatchell, B. S. Furnis, A. J.Hannaford, P. W. G. Smith, (Prentice Hall) 5^(th) Edition (1996),March's Advanced Organic Chemistry: Reactions, Mechanisms, andStructure, Michael B. Smith, Jerry March, (Wiley-Interscience) 5^(1h)Edition (2007), and references therein, which are incorporated byreference herein. However, these may not be the only means by which tosynthesize or obtain the desired compounds.

Another aspect of the invention comprises a compound used in the methodof the present invention as a pharmaceutical composition.

As used herein, the term “pharmaceutically active agent” means anysubstance or compound suitable for administration to a subject andfurnishes biological activity or other direct effect in the treatment,cure, mitigation, diagnosis, or prevention of disease, or affects thestructure or any function of the subject. Pharmaceutically active agentsinclude, but are not limited to, substances and compounds described inthe Physicians' Desk Reference (PDR Network, LLC; 64th edition; Nov. 15,2009) and “Approved Drug Products with Therapeutic EquivalenceEvaluations” (U.S. Department Of Health And Human Services, 30^(th)edition, 2010), which are hereby incorporated by reference.Pharmaceutically active agents which have pendant carboxylic acid groupsmay be modified in accordance with the present invention using standardesterification reactions and methods readily available and known tothose having ordinary skill in the art of chemical synthesis. Where apharmaceutically active agent does not possess a carboxylic acid group,the ordinarily skilled artisan will be able to design and incorporate acarboxylic acid group into the pharmaceutically active agent whereesterification may subsequently be carried out so long as themodification does not interfere with the pharmaceutically active agent'sbiological activity or effect.

The compounds used in the method of the present invention may be in asalt form. As used herein, a “salt” is a salt of the instant compoundswhich has been modified by making acid or base salts of the compounds.In the case of compounds used to treat an infection or disease caused bya pathogen, the salt is pharmaceutically acceptable. Examples ofpharmaceutically acceptable salts include, but are not limited to,mineral or organic acid salts of basic residues such as amines; alkalior organic salts of acidic residues such as phenols. The salts can bemade using an organic or inorganic acid. Such acid salts are chlorides,bromides, sulfates, nitrates, phosphates, sulfonates, formates,tartrates, maleates, malates, citrates, benzoates, salicylates,ascorbates, and the like. Phenolate salts are the alkaline earth metalsalts, sodium, potassium or lithium. The term “pharmaceuticallyacceptable salt” in this respect, refers to the relatively non-toxic,inorganic and organic acid or base addition salts of compounds of thepresent invention. These salts can be prepared in situ during the finalisolation and purification of the compounds of the invention, or byseparately reacting a purified compound of the invention in its freebase or free acid form with a suitable organic or inorganic acid orbase, and isolating the salt thus formed. Representative salts includethe hydrobromide, hydrochloride, sulfate, bisulfate, phosphate, nitrate,acetate, valerate, oleate, palmitate, stearate, laurate, benzoate,lactate, phosphate, tosylate, citrate, maleate, fumarate, succinate,tartrate, napthylate, mesylate, glucoheptonate, lactobionate, andlaurylsulphonate salts and the like. (See, e.g., Berge et al. (1977)“Pharmaceutical Salts”, J. Pharm. Sci. 66:1-19).

As used herein, “treating” means preventing, slowing, halting, orreversing the progression of a disease or infection. Treating may alsomean improving one or more symptoms of a disease or infection.

The compounds used in the method of the present invention may beadministered in various forms, including those detailed herein. Thetreatment with the compound may be a component of a combination therapyor an adjunct therapy, i.e. the subject or patient in need of the drugis treated or given another drug for the disease in conjunction with oneor more of the instant compounds. This combination therapy can besequential therapy where the patient is treated first with one drug andthen the other or the two drugs are given simultaneously. These can beadministered independently by the same route or by two or more differentroutes of administration depending on the dosage forms employed.

As used herein, a “pharmaceutically acceptable carrier” is apharmaceutically acceptable solvent, suspending agent or vehicle, fordelivering the instant compounds to the animal or human. The carrier maybe liquid or solid and is selected with the planned manner ofadministration in mind. Liposomes are also a pharmaceutically acceptablecarrier.

The dosage of the compounds administered in treatment will varydepending upon factors such as the pharmacodynamic characteristics of aspecific chemotherapeutic agent and its mode and route ofadministration; the age, sex, metabolic rate, absorptive efficiency,health and weight of the recipient; the nature and extent of thesymptoms; the kind of concurrent treatment being administered; thefrequency of treatment with; and the desired therapeutic effect.

A dosage unit of the compounds used in the method of the presentinvention may comprise a single compound or mixtures thereof withadditional antibacterial agents. The compounds can be administered inoral dosage forms as tablets, capsules, pills, powders, granules,elixirs, tinctures, suspensions, syrups, and emulsions. The compoundsmay also be administered in intravenous (bolus or infusion),intraperitoneal, subcutaneous, or intramuscular form, or introduceddirectly, e.g. by injection, topical application, or other methods, intoor onto a site of infection, all using dosage forms well known to thoseof ordinary skill in the pharmaceutical arts.

The compounds used in the method of the present invention can beadministered in admixture with suitable pharmaceutical diluents,extenders, excipients, or carriers (collectively referred to herein as apharmaceutically acceptable carrier) suitably selected with respect tothe intended form of administration and as consistent with conventionalpharmaceutical practices. The unit will be in a form suitable for oral,rectal, topical, intravenous or direct injection or parenteraladministration. The compounds can be administered alone or mixed with apharmaceutically acceptable carrier. This carrier can be a solid orliquid, and the type of carrier is generally chosen based on the type ofadministration being used. The active agent can be co-administered inthe form of a tablet or capsule, liposome, as an agglomerated powder orin a liquid form. Examples of suitable solid carriers include lactose,sucrose, gelatin and agar. Capsule or tablets can be easily formulatedand can be made easy to swallow or chew; other solid forms includegranules, and bulk powders. Tablets may contain suitable binders,lubricants, diluents, disintegrating agents, coloring agents, flavoringagents, flow-inducing agents, and melting agents. Examples of suitableliquid dosage forms include solutions or suspensions in water,pharmaceutically acceptable fats and oils, alcohols or other organicsolvents, including esters, emulsions, syrups or elixirs, suspensions,solutions and/or suspensions reconstituted from non-effervescentgranules and effervescent preparations reconstituted from effervescentgranules. Such liquid dosage forms may contain, for example, suitablesolvents, preservatives, emulsifying agents, suspending agents,diluents, sweeteners, thickeners, and melting agents. Oral dosage formsoptionally contain flavorants and coloring agents. Parenteral andintravenous forms may also include minerals and other materials to makethem compatible with the type of injection or delivery system chosen.

Techniques and compositions for making dosage forms useful in thepresent invention are described in the following references: 7 ModernPharmaceutics, Chapters 9 and 10 (Banker & Rhodes, Editors, 1979);Pharmaceutical Dosage Forms: Tablets (Lieberman et al., 1981); Ansel,Introduction to Pharmaceutical Dosage Forms 2nd Edition (1976);Remington's Pharmaceutical Sciences, 17th ed. (Mack Publishing Company,Easton, Pa., 1985); Advances in Pharmaceutical Sciences (DavidGanderton, Trevor Jones, Eds., 1992); Advances in PharmaceuticalSciences Vol. 7. (David Ganderton, Trevor Jones, James McGinity, Eds.,1995); Aqueous Polymeric Coatings for Pharmaceutical Dosage Forms (Drugsand the Pharmaceutical Sciences, Series 36 (James McGinity, Ed., 1989);Pharmaceutical Particulate Carriers: Therapeutic Applications: Drugs andthe Pharmaceutical Sciences, Vol 61 (Alain Rolland, Ed., 1993); DrugDelivery to the Gastrointestinal Tract (Ellis Horwood Books in theBiological Sciences. Series in Pharmaceutical Technology; J. G. Hardy,S. S. Davis, Clive G. Wilson, Eds.); Modem Pharmaceutics Drugs and thePharmaceutical Sciences, Vol 40 (Gilbert S. Banker, Christopher T.Rhodes, Eds.). All of the aforementioned publications are incorporatedby reference herein.

Tablets may contain suitable binders, lubricants, disintegrating agents,coloring agents, flavoring agents, flow-inducing agents, and meltingagents. For instance, for oral administration in the dosage unit form ofa tablet or capsule, the active drug component can be combined with anoral, non-toxic, pharmaceutically acceptable, inert carrier such aslactose, gelatin, agar, starch, sucrose, glucose, methyl cellulose,magnesium stearate, dicalcium phosphate, calcium sulfate, mannitol,sorbitol and the like. Suitable binders include starch, gelatin, naturalsugars such as glucose or beta-lactose, corn sweeteners, natural andsynthetic gums such as acacia, tragacanth, or sodium alginate,carboxymethylcellulose, polyethylene glycol, waxes, and the like.Lubricants used in these dosage forms include sodium oleate, sodiumstearate, magnesium stearate, sodium benzoate, sodium acetate, sodiumchloride, and the like. Disintegrators include, without limitation,starch, methyl cellulose, agar, bentonite, xanthan gum, and the like.

The compounds used in the method of the present invention may also beadministered in the form of liposome delivery systems, such as smallunilamellar vesicles, large unilamallar vesicles, and multilamellarvesicles. Liposomes can be formed from a variety of phospholipids, suchas cholesterol, stearylamine, or phosphatidylcholines. The compounds maybe administered as components of tissue-targeted emulsions.

The compounds used in the method of the present invention may also becoupled to soluble polymers as targetable drug carriers or as a prodrug.Such polymers include polyvinylpyrrolidone, pyran copolymer,polyhydroxylpropylmethacrylamide-phenol,polyhydroxyethylaspartamidephenol, or polyethyleneoxide-polylysinesubstituted with palmitoyl residues. Furthermore, the compounds may becoupled to a class of biodegradable polymers useful in achievingcontrolled release of a drug, for example, polylactic acid, polyglycolicacid, copolymers of polylactic and polyglycolic acid, polyepsiloncaprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals,polydihydropyrans, polycyanoacylates, and crosslinked or amphipathicblock copolymers of hydrogels.

Gelatin capsules may contain the active ingredient compounds andpowdered carriers, such as lactose, starch, cellulose derivatives,magnesium stearate, stearic acid, and the like. Similar diluents can beused to make compressed tablets. Both tablets and capsules can bemanufactured as immediate release products or as sustained releaseproducts to provide for continuous release of medication over a periodof hours. Compressed tablets can be sugar coated or film coated to maskany unpleasant taste and protect the tablet from the atmosphere, orenteric coated for selective disintegration in the gastrointestinaltract.

For oral administration in liquid dosage form, the oral drug componentsare combined with any oral, non-toxic, pharmaceutically acceptable inertcarrier such as ethanol, glycerol, water, and the like. Examples ofsuitable liquid dosage forms include solutions or suspensions in water,pharmaceutically acceptable fats and oils, alcohols or other organicsolvents, including esters, emulsions, syrups or elixirs, suspensions,solutions and/or suspensions reconstituted from non-effervescentgranules and effervescent preparations reconstituted from effervescentgranules. Such liquid dosage forms may contain, for example, suitablesolvents, preservatives, emulsifying agents, suspending agents,diluents, sweeteners, thickeners, and melting agents.

Liquid dosage forms for oral administration can contain coloring andflavoring to increase patient acceptance. In general, water, a suitableoil, saline, aqueous dextrose (glucose), and related sugar solutions andglycols such as propylene glycol or polyethylene glycols are suitablecarriers for parenteral solutions. Solutions for parenteraladministration preferably contain a water soluble salt of the activeingredient, suitable stabilizing agents, and if necessary, buffersubstances. Antioxidizing agents such as sodium bisulfite, sodiumsulfite, or ascorbic acid, either alone or combined, are suitablestabilizing agents. Also used are citric acid and its salts and sodiumEDTA. In addition, parenteral solutions can contain preservatives, suchas benzalkonium chloride, methyl- or propyl-paraben, and chlorobutanol.Suitable pharmaceutical carriers are described in Remington'sPharmaceutical Sciences, Mack Publishing Company, a standard referencetext in this field.

The compounds used in the method of the present invention may also beadministered in intranasal form via use of suitable intranasal vehicles,or via transdermal routes, using those forms of transdermal skin patcheswell known to those of ordinary skill in that art. To be administered inthe form of a transdermal delivery system, the dosage administrationwill generally be continuous rather than intermittent throughout thedosage regimen.

Parenteral and intravenous forms may also include minerals and othermaterials to make them compatible with the type of injection or deliverysystem chosen.

The compounds and compositions of the present invention can beadministered in oral dosage forms as tablets, capsules, pills, powders,granules, elixirs, tinctures, suspensions, syrups, and emulsions. Thecompounds may also be administered in intravenous (bolus or infusion),intraperitoneal, subcutaneous, or intramuscular form, or introduceddirectly, e.g. by topical administration, injection or other methods, tothe afflicted area, such as a wound, including ulcers of the skin, allusing dosage forms well known to those of ordinary skill in thepharmaceutical arts.

Specific examples of pharmaceutical acceptable carriers and excipientsthat may be used to formulate oral dosage forms of the present inventionare described in U.S. Pat. No. 3,903,297 to Robert, issued Sep. 2, 1975.Techniques and compositions for making dosage forms useful in thepresent invention are described-in the following references: 7 ModernPharmaceutics, Chapters 9 and 10 (Banker & Rhodes, Editors, 1979);Pharmaceutical Dosage Forms: Tablets (Lieberman et al., 1981); Ansel,Introduction to Pharmaceutical Dosage Forms 2nd Edition (1976);Remington's Pharmaceutical Sciences, 17th ed. (Mack Publishing Company,Easton, Pa., 1985); Advances in Pharmaceutical Sciences (DavidGanderton, Trevor Jones, Eds., 1992); Advances in PharmaceuticalSciences Vol 7. (David Ganderton, Trevor Jones, James McGinity, Eds.,1995); Aqueous Polymeric Coatings for Pharmaceutical Dosage Forms (Drugsand the Pharmaceutical Sciences, Series 36 (James McGinity, Ed., 1989);Pharmaceutical Particulate Carriers: Therapeutic Applications: Drugs andthe Pharmaceutical Sciences, Vol 61 (Alain Rolland, Ed., 1993); DrugDelivery to the Gastrointestinal Tract (Ellis Horwood Books in theBiological Sciences. Series in Pharmaceutical Technology; J. G. Hardy,S. S. Davis, Clive G. Wilson, Eds.); Modem Pharmaceutics Drugs and thePharmaceutical Sciences, Vol 40 (Gilbert S. Banker, Christopher T.Rhodes, Eds.). All of the aforementioned publications are incorporatedby reference herein.

The term “prodrug” as used herein refers to any compound that whenadministered to a biological system generates the compound of theinvention, as a result of spontaneous chemical reaction(s), enzymecatalyzed chemical reaction(s), photolysis, and/or metabolic chemicalreaction(s). A prodrug is thus a covalently modified analog or latentform of a compound of the invention.

The active ingredient can be administered orally in solid dosage forms,such as capsules, tablets, powders, and chewing gum; or in liquid dosageforms, such as elixirs, syrups, and suspensions, including, but notlimited to, mouthwash and toothpaste. It can also be administeredparentally, in sterile liquid dosage forms.

Solid dosage forms, such as capsules and tablets, may be enteric coatedto prevent release of the active ingredient compounds before they reachthe small intestine. Materials that may be used as enteric coatingsinclude, but are not limited to, sugars, fatty acids, waxes, shellac,cellulose acetate phthalate (CAP), methyl acrylate-methacrylic acidcopolymers, cellulose acetate succinate, hydroxy propyl methyl cellulosephthalate, hydroxy propyl methyl cellulose acetate succinate(hypromellose acetate succinate), polyvinyl acetate phthalate (PVAP),and methyl methacrylate-methacrylic acid copolymers.

The compounds and compositions of the invention can be coated ontostents for temporary or permanent implantation into the cardiovascularsystem of a subject.

The compounds of the present invention can be synthesized according togeneral Schemes. Variations on the following general synthetic methodswill be readily apparent to those skilled in the art and are deemed tobe within the scope of the present invention.

Each embodiment disclosed herein is contemplated as being applicable toeach of the other disclosed embodiments. Thus, all combinations of thevarious elements described herein are within the scope of the invention.

This invention will be better understood by reference to theExperimental Details which follow, but those skilled in the art willreadily appreciate that the specific experiments detailed are onlyillustrative of the invention as described more fully in the claimswhich follow thereafter.

EXPERIMENTAL DETAILS

Recombinant HDAC1 and HDAC6 are used to evaluate the selectiveinhibitory potency of each compound. Cell based assays: Normal cells(Human Foreskin Fibroblast cells), LNCaP (human prostate cancer cells),MCF-7 (human breast cancer cells, A549 (human adenocarcinoma of lungcells) and ARP-1 (human multiple myeloma cells) are used in theseassays. Cells were cultured for up to 72 hr without and with thepotential HDAC6-selective inhibitor. SAHA was used as a control. Cellnumber and cell viability were determined by enumeration. Proteins wereextracted from cells and assayed for accumulation of acetylated tubulinand acetylated histones. All methods are described in Namdar et al.,PNAS, 2010, 107:20003-8. In vivo animal studies: Potential HDAC6inhibitor compounds are further assayed by administration to mice for upto 5 days with daily injections. Animals are sacrificed and tissues areanalyzed for accumulation of acetylated tubulin and acetylated histones.

8-Aminoquinoline, aniline, glycolaldehyde dimer, sodiumtriacetoxyborohydride, tert-butylchlorodimethylsilane (TBDMS-Cl),potassium cyanide, NH₂OH, trifluoroacetic acid (TFA), dichloroethane(DCE), dichloromethne (DCM),1-Ethyl-3-(3-dimethyllaminopropyl)carbodiimide hydrochloride (EDC),sodium sulfate (anhydrous), calcium hypochlorite, molecular sieves (4Å), NH₄Cl, NaCl, MeOH, NaHCO₃, THF, hydrochloric acid, acetic acid,CDCl₃, CD₃OD, and hexanes were used as received without furtherpurification. Purification of product mixtures was carried out by columnusing silica gel with 40-60 Å particle size or preparativechromatography using silica gel 60F 254 TLC-plates. TLC was carried outusing silica gel 60F 254 TLC-plates. Proton NMR data were acquired at400 MHz and ¹³C NMR data were acquired at 100.6 MHz.

Those having ordinary skill in the art of organic synthesis willappreciate that modifications to general procedures and synthetic routescontained in this application can be used to yield additionalderivatives and structurally diverse compounds. Suitable organictransformations are described in in March's Advanced Organic Chemistry:Reactions, Mechanisms, and Structure (Wiley-Interscience; 6^(th)edition, 2007), the content of which is hereby incorporated byreference.

Example 1. Synthesis of Compound 8

HDAC inhibitor 8 was prepared according to the protocols shown in Scheme1 and Scheme 2. Methyl ester 5 was prepared by treatment of mesylate 2with 2-(tert-butyldimethylsiloxy) ethanamine 4 in the presence oftriethylamine. Amine 5 was coupled to 2-phenylacetyl chloride to formamide 7. The methyl ester of 7 was converted directly, using aqueoushydroxylamine, to the corresponding hydroxamic acid, which wasdeprotected with 2% aqueous HCl to afford compound 8.

Scheme 1: Reagents and conditions: a) Et₃N, MsCl, CH₂Cl₂, 0° C.-rt; b)Imidazole, TBSCl, CH₂Cl₂, 0° C.-rt; c) 2, 4, Et₃N, DMF, rt.

Methyl 4-(((methylsulfonyl)oxy)methyl)benzoate (2)

Triethylamine (1.3 mL, 9.0 mmol) was added drop wise over 1 min to asolution of methanesulfonyl chloride (0.55 mL, 7.2 mmol), methyl4-(hydroxymethyl)-benzoate (1.0 g, 6.0 mmol), and CH₂Cl₂ (40 mL) at 0°C. The resulting solution was allowed to warm to rt and maintained for 1hr. Water (2 ml) was added and the mixture stirred for 15 min. Theorganic layer was extracted with NaHCO₃ (10 ml×2), H₂O (10 mL×2), andbrine (10 mL). The resulting solution was dried (MgSO₄), filtered, andconcentrated to yield a white solid. ¹H NMR (400 MHz, CDCl₃) δ 3.13 (s,3H), 3.89 (s, 3H), 4.9 (s, 2H), 7.52 (d, J=8.4 Hz, 2H), 8.06 (d, J=8.4Hz, 2H); ¹³C NMR (100 MHz, CDCl₃) δ 166.1, 137.2, 131.5, 130.1, 127.5,75.0, 52.3, 39.4; [M+H]⁺=245.5 (APCI+).

2-((tert-butyldimethylsilyl)oxy)ethan-1-amine (4)

A solution of tert-butyldimethylchlorosilane (3.6 g, 24 mmol) anddichloromethane (10 mL) was added drop wise over 3 min to a stirredsolution of ethanolamine (1.22 g, 20 mmol), imidazole (2.04 g, 30 mmol),and dichloromethane (20 mL) at room temperature, and the resultingmixture was stirred at room temperature for 1 h., water (20 mL) wasadded, and the phases were separated. The aqueous phase was extractedwith dichloromethane (2×20 mL), and the combined organic phases weredried (MgSO₄), filtered and concentrated in vacuo to give the titlecompound (3.50 g, 100%) as pale yellow oil. ¹H NMR (400 MHz, CDCl₃) δ3.64 (t, J=5.0, 2H), 3.05 (br s, 2H), 2.80 (t, J=5.0, 2H), 0.90 (s, 9H),0.06 (s, 6H); ¹³C NMR (100 MHz, CDCl₃) δ 64.7, 44.1, 25.9, 18.3, −3.4;[M+H]⁺=176.6 (APCI+).

Methyl 4-(((2-((tert-butyldimethylsilyl)oxy)ethyl)amino) methyl)benzoate (5)

2-(tert-Butyldimethylsiloxy)ethanamine 4, (1.54 g, 8.64 mmol) was addedto a solution of 4-methanesulfonyloxymethylbenzoic acid methyl ester(1.76 g, 7.2 mmol) and triethylamine (0.98 mL, 7.2 mmol) in DMF (10 mL),and then the reaction mixture was stirred at room temperature for 2hours. Saturated aq NaHCO₃ solution (150 mL) was added, and then thewhole reaction mixture was extracted with chloroform (100 mL×3). Theorganic layer was dried. Evaporation and purification by silica gelcolumn chromatography (EtOAc:n-hexanes, 1:4) gave 5 as a yellowish oil(1.82 g, 78% yield): ¹H NMR (400 MHz, CDCl₃): 7.94 (d, J=8.4 Hz, 2H),7.34 (d, J=8.0 Hz, 2H), 3.85 (s, 3H), 3.81 (s, 2H), 3.68 (t, J=2.67 (t,J=5.2 Hz, 2H) 0.76 (s, 9H), δ 0.02 (s, 6H); ¹³C NMR (CHCl₃, 100 MHz): δ167.1, 136.8, 132.5, 130.3, 127.5, 75.0, 64.7, 52.3, 44.1, 25.9, 18.8,−3.4; [M+H]⁺=324.2 (APCI+).

Scheme 2: Reagents and conditions: d) 5, 6, Et₃N, CH₂Cl₂, 0° C.-rt; e)50% (w/w) aq. NH₂OH, MeOH, rt; f) 2% aq. HCl, MeOH, 0° C.-rt.

Methyl 4-((N-(2-((tert-butyldimethylsilyl)oxy)ethyl)-2-phenylacetamido)methyl)benzoate (7)

2-phenylacetyl chloride (0.44 mL, 3.3 mmol) was added drop wise to asolution of 5 (0.89 g, 2.75 mmol) in 8 mL dry dichloromethane containingtriethylamine (0.7 mL, 4.95 mmol) at 0° C. The resulting solution wasallowed to warm to rt and stirred for 4 hr. After completion of thereaction (by TLC), added 30 mL dichloromethane and washed with sat.ammonium chloride (30 mL×2) and brine (30 mL×2). The organic layer wasdried (MgSO₄), filtered, and concentrated in vacuo. The Crude compoundwas purified on silica gel column (EtOAc:Hexanes, 1:5) to give thecompound 7 (0.87 g, 72%). ¹H NMR (CHCl₃, 400 MHz): δ 7.91 (d, J=8.2, Hz,2H), 7.38 (m, 3H), 7.15 (m, 4H), 3.91 (s, 3H), 3.80 (m, 4H), 3.50 (s,2H), 0.85 (s, 9H), 0.02 (s, 6H); ¹³C NMR (CHCl₃, 100 MHz): δ 170.2,167.0, 142.9, 140.8, 129.6, 129.5, 129.1, 128.6, 128.5, 128.0, 60.1,52.1, 52.0, 41.4, 39.9, 25.8, 18.2, −5.4; [M+H]⁺=442.6 (APCI+).

N-hydroxy-4-((N-(2-hydroxyethyl)-2-phenylacetamido) methyl) benzamide(8)

Hydroxylamine (0.5 mL, 50% water solution) was added to a solution of 7,(500 mg, 1.13 mmol) in methanol (5 mL). Reaction mixture was treatedwith cat. amount of KCN (˜0.5 mg) and stirred at room temperature inargon atmosphere for 16 h. Then solution was acidified by NH₄Cl/HClsolution to pH˜4.5. The mixture was diluted with mixed solvent(CHCl₃:i-PrOH=4:1, 10 mL) and washed with sat. NH₄Cl. The organic layerwas dried (anhydrous sodium sulfate) and concentrated in vacuo. Crudematerial was dissolved in MeOH (8 mL) and added 4% (v/v) HCl in MeOH (8mL) drop wise at 0° C. The reaction mixture was stirred at roomtemperature for 3 hrs. Once the starting material is completelyconsumed, added solid NaHCO3 (˜100 mg) to neutralize excess HCl.Organics was filtered, dried over Na₂SO₄ and evaporated in vacuo. Crudematerial was purified on silica gel column (MeOH/CH₂Cl₂=1/10) to givethe titled compound 8. (120 mg, 32.2%) ¹H NMR (CD₃OD, 400 MHz): δ7.75-7.69 (m, 2H), 7.36-7.22 (m, 7H), 4.83 (s, 1H), 4.75 (s, 1H), 3.96(s, 1H), 3.78 (s, 1H), 3.72-3.67 (m, 2H), 3.52 (m, 2H); ¹³C NMR (CD₃OD,100 MHz) δ 173.2, 173.1, 166.5, 166.3, 141.6, 140.9, 135.2, 134.8,131.4, 131.1, 128.7, 128.6, 128.3, 127.4, 127.3, 127.0, 126.5, 59.3,59.1, 52.4, 49.6, 48.7, 48.3, 40.2, 39.9; [M+H]⁺=329.1 (APCI+); HRMScalcd for C₁₈H₂₁N₂O₄ [M+H]⁺ 329.1501, found 329.1494.

Example 2. Synthesis of Compound 11

HDAC inhibitor 11 was prepared according to the protocols shown inScheme 3. Amine 5 was coupled to benzoyl chloride to form amide 10. Themethyl ester of 10 was converted directly, using aqueous hydroxylamine,to the corresponding hydroxamic acid, which was deprotected with 2%aqueous HCl to afford compound 11.

Reagents and conditions: a) 5, 7, Et₃N, CH₂Cl₂, 0° C.-rt; b) 50% (w/w)aq. NH₂OH, MeOH, rt; f) 2% aq. HCl, MeOH, 0° C.-rt.

Methyl 4-((N-(2-((tert-butyldimethylsilyl)oxy)ethyl)benzamido)methyl)benzoate (10)

Benzoyl chloride (0.73 mL, 6.31 mmol) was added drop wise to a solutionof 5 (1.7 g, 5.26 mmol) in 15 mL dry dichloromethane containingtriethylamine (1.3 mL, 9.5 mmol) at 0° C. Then the reaction mixture isallowed to reach room temperature and stirred for 4 hrs. Aftercompletion of the reaction (by TLC), added 30 mL dichloromethane andwashed with sat. ammonium chloride (30 mL×2) followed by sat. sodiumchloride (30 mL×2). The organic layer was dried with anhydrous NaSO₄,filtered, and removed under vacuum. Crude compound was purified onsilica gel column (EtOAc:Hexanes, 1:5) to give the compound 10 (0.92 g,70%). ¹H NMR (CHCl₃, 400 MHz): δ 7.91 (d, J=8.2, Hz, 2H), 7.38 (m, 3H),7.15 (m, 4H), 3.91 (s, 3H), 3.80 (m, 4H), 3.60 (s, 2H), 0.85 (s, 9H),0.02 (s, 6H); ¹³C NMR (CHCl₃, 100 MHz): δ 171.2, 168.0, 142.4, 140.8,129.6, 129.5, 129.1, 128.6, 128.5, 128.0, 54.1, 53.0, 41.4, 39.9, 25.8,18.2, −5.4; [M+H]⁺=428.4 (APCI+).

N-hydroxy-4-((N-(2-hydroxyethyl)-2-benzamido)methyl)benzamide (11)

Hydroxylamine (0.5 mL, 50% water solution) was added to a solution of10, (500 mg, 1.13 mmol) in methanol (5 mL). Reaction mixture was treatedwith cat. amount of KCN (0.5 mg) and stirred at room temperature inargon atmosphere for 16 h. Then solution was acidified by NH₄Cl/HClsolution to pH ˜4.5. The mixture was diluted with mixed solvent(CHCl₃:i-PrOH=4:1, 10 mL) and washed with sat. NH₄Cl. The organic layerwas dried (anhydrous sodium sulfate) and concentrated in vacuo. Crudematerial was dissolved in MeOH (8 mL) and added 4% (v/v) HCl in MeOH (8mL) drop wise at 0° C. The reaction mixture was stirred at roomtemperature for 3 hrs. Once the starting material is completelyconsumed, added solid NaHCO₃ (˜100 mg) to neutralize excess HCl.Organics was filtered, dried over Na2SO4 and evaporated in vacuo. Crudematerial was purified on silica gel column (MeOH:CH₂Cl₂=1:10) to givethe titled compound 11. (140 mg, 38.1%) ¹H NMR (CD₃OD, 400 MHz): δ7.80-7.75 (m, 2H), 7.52-7.45 (m, 6H), 7.30 (m, 1H), 4.73 (s, 1H), 3.84(s, 1H), 3.61 (s, 2H), 3.42-3.39 (m, 1H); ¹³C NMR (CD₃OD, 100 MHz) δ173.5, 166.5, 141.4, 140.8, 136.1, 135.9, 131.5, 131.2, 129.4, 128.3,127.6, 127.3, 127.2, 126.8, 126.6, 126.2, 59.1, 58.7, 53.6, 48.3;[M+H]⁺=315.1 (APCI+); HRMS calcd for C₁₇H₁₉N₂O₄ [M+H]⁺ 315.1345, found315.1337.

Example 3. Synthesis of Compound 23

HDAC inhibitor 23 was prepared according to the protocols shown inSchemes 4 and 5. Amine 20 was coupled to acid 18 to form amide 21. Themethyl ester of 21 was converted directly, using aqueous hydroxylamine,to the corresponding hydroxamic acid, which was deprotected with 2%aqueous HCl to afford compound 23.

Reagents and conditions: a) MeOH/cat. H₂SO₄ 70° C. 6 h; b) NBS,(PhCO₂)₂, CCl4, 80° C., 12 h; c) NaCN, DMF/H2O, 70° C., 4 h; d) aq NaOH(6N), MeOH, 90° C. 12 h; e) MeOH/cat. H₂SO₄ 90° C. 18 h; f) MeOH, H₂O,K₂CO₃, rt, 4 h.

Methyl 5-methyl-2-thiophenecarboxylate (13)

5-Methyl-thiophene-2-carboxylic acid (5 g, 35 mmol) was refluxed inH₂SO₄ in MeOH (2 M) for 6 h. The reaction was neutralized with NaOH (10N) at 0° C., and the methyl ester was extracted with DCM affording 4.85g (89%) of 5-methylthiophene-2-carboxylic acid methyl ester. ¹H NMR(CHCl₃, 400 MHz): δ 7.78 (d, J=3.8, 1H), 6.82 (d, J=3.8, 1H), 3.90 (s,3H), 2.21 (s, 3H); ¹³C NMR (CHCl₃, 100 MHz): δ 162.1, 144.2, 137.5,132.2, 129.2, 53.0, 18.9; [M+H]+=157.12 (APCI+).

Methyl 5-(bromomethyl)thiophene-2-carboxylate (14)

The methyl ester 13, (2.4 g, 15.5 mmol) was refluxed in CCl₄ in thepresence of NBS (3 g, 17 mmol) and benzoyl peroxide (121 mg, 0.03 equiv)for 12 h. The reaction was cooled to 0° C. and filtered. Organics wasfiltered, dried over Na2SO₄ and evaporated in vacuo. Crude material waspurified on silica gel column (EtOAc:Hexanes=1:5) to give the titledcompound 14. (2.9 g, 82%). ¹H NMR (CHCl₃, 400 MHz): δ 7.64 (d, J=3.6,1H), 7.10 (m, 18), 3.90 (s, 3H), 3.89 (s, 3H); ¹³C NMR (CHCl₃, 100 MHz):δ 162.4, 149.8, 135.5, 130.2, 124.8, 52.4, 23.4; [M+H]⁺=⁺=235.1 (APCI+).

Methyl 5-(cyanomethyl)thiophene-2-carboxylate (15)

A solution of NaCN (787 mg, 16.0 mmol) in water (2 mL) was added dropwise to a solution of Methyl 5-(bromomethyl)thiophene-2-carboxylate 14,(2.6 g, 11.06 mmol) in DMF (18 mL) at 0° C. in argon atmosphere. Thereaction mixture was stirred for 4 hrs. After completion of reaction(TLC) added saturated ammonium chloride solution (50 mL) and extractedwith dichloromethane (30 mL×3). Organics was combined, dried over Na₂SO₄and evaporated in vacuo. Crude material was purified on silica gelcolumn (EtOAc:Hexanes=1:4) to give the titled compound 15. (1.1 g, 55%).¹H NMR (CHCl₃, 400 MHz): δ 7.62 (d, J=3.6, 1H), 7.10 (m, 1H), 4.31 (s,2H), 3.89 (s, 3H); ¹³C NMR (CHCl₃, 100 MHz): δ 164.4, 138.6, 136.2,133.2, 127.1, 62.4, 20.4, 17.0; [M+H]+=182.3 (APCI+).

5-(carboxymethyl)thiophene-2-carboxylic acid (16)

A solution of methyl 5-(cyanomethyl)thiophene-2-carboxylate 15, (500 mg,2.76 mmol) in 6M Sodium hydroxide (10 mL) and methanol (10 mL) washeated at 90° C. overnight. After concentrating the reaction mixture,the aqueous layer was washed with dichloromethane (20 mL×2), thenacidified to pH-3 with 12M HCl. The aqueous solution was extracted withethyl acetate (20 mL×2). Organics was combined, dried over Na₂SO₄ andevaporated in vacuo to give titled compound 16. (650 mg, 80%). ¹H NMR(CHCl₃, 400 MHz): δ 7.70 (d, J=3.6, 1H), 6.91 (m, 1H), 4.03 (s, 2H); ¹³CNMR (CHCl₃, 100 MHz): δ 178.4, 164.3, 145.5, 138.3, 132.2, 127.5, 38.5;[M+H]⁺=187.2 (APCI+).

Methyl 5-(2-methoxy-2-oxoethyl)thiophene-2-carboxylate (17)

A solution of 5-(carboxymethyl)thiophene-2-carboxylic acid 16, (500 mg,2.68 mmol) and H₂SO₄ (2 mL) in methanol (20 mL) was heated at 90° C.overnight. After concentrating the reaction mixture, the crude was takeninto EtOAc (30 mL) and washed with sat. NaHCO₃ (30 mL). Then the organiclayer was dried over Na₂SO₄ and evaporated in vacuo. Crude material waspurified on silica gel column (EtOAc:Hexanes=1:6) to give the titlecompound 17. (525 mg, 90%). ¹H NMR (CHCl₂, 400 MHz): δ 7.61 (d, J=3.6,1H), 7.01 (m, 1H), 3.91 (s, 3H), 3.80 (s, 2H), 3.62 (s, 3H); ¹³C NMR(CHCl₃, 100 MHz): δ 172.4, 163.5, 141.5, 137.3, 130.2, 125.5, 53.5,53.0, 37.5; [M+H]⁺⁼215.4 (APCI+).

2-(5-(methoxycarbonyl)thiophen-2-yl)acetic acid (18)

A solution of methyl 5-(2-methoxy-2-oxoethyl)thiophene-2-carboxylate 17,(500 mg, 2.33 mmol) and K₂CO₃ (572 mg, 3.49 mmol) in water/methanolmixture (15 mL, 1:1) was stirred at room temperature 4 hrs. Afterconcentrating the reaction mixture to 5 mL diluted with water (20 mL).Then the aqueous layer was washed with dichloromethane (20 mL×2), andacidified to pH-3 with 12M HCl. The aqueous solution was extracted withethyl acetate (20 mL×2). Organics was combined, dried over Na₂SO₄ andevaporated in vacuo to give titled compound 18. (400 mg, 85%). ¹H NMR(CHCl₃, 400 MHz): δ 7.60 (d, J=3.6, 1H), 6.80 (m, 1H), 3.80 (s, 2H),3.75 (s, 3H); ¹³C NMR (CHCl₃, 100 MHz): δ 178.1, 163.3, 145.1, 131.2,126.5, 53.4, 37.5; [M+H]⁺=201.2 (APCI+).

Reagents and conditions: a) Imidazole, TBSCl, CH₂Cl₂, rt; b) 20, EDCI,Et₃N, CH₂Cl₂, rt, 18 h; 50%; ci) (w/w) aq. NH₂OH, MeOH, rt; d) 2% aq.HCl, MeOH, 0° C.-rt, 3 h.

N-(2-((tert-butyldimethylsilyl)oxy)ethyl)aniline (20)

TBDMS-Cl (1.28 g, 8.02 mmol) and imidazole (1.45 g, 21.86 mmol) wasadded to a solution containing 2-(phenylamino)ethanol 19, (1.00 g, 7.29mmol) in CH₂Cl₂ (10 mL). The reaction mixture was stirred at roomtemperature in argon atmosphere for 3 h. Then the reaction was quenchedwith sat. NH₄Cl. and washed with water (10 mL×2) and brine (10 mL×2).The organic layer was dried (anhydrous sodium sulfate) and concentratedin vacuo. The crude product was chromatographed on silica gel(Hexanes/EtOAc, 7:1) to yield target compound 20. Yield 1.689 g, 92%.R_(f)=0.60, ¹H NMR (CHCl₃, 400 MHz): δ 7.22 (dd, J=8.8, 7.4 Hz, 2H),6.76 (t, J=7.4 Hz, 1H), 6.68 (d, J=8.8, 2H), 4.09 (br s, 1H), 3.86 (t,J=5.2 Hz, 2H), 3.26 (t, J=5.2 Hz, 2H), 0.95 (s, 9H), 0.11 (s, 6H); ¹³CNMR (CHCl₃, 100 MHz): δ 148.4, 129.2, 117.5, 113.2, 61.6, 46.0, 25.9,18.3, −5.3; [M+H]⁺=252.12 (APCI+).

Methyl 5-(2-((2-((tert butyldimethylsilyl)oxy)ethyl) (phenyl)amino)-2-oxoethyl)thiophene-2-carboxylate) (21)

EDCI (291.0 mg, 1.52 mmol) was added to a solution containingN-(2-((tert-butyldimethyl silyl) oxy)ethyl)aniline 20, (390 mg, 1.60mmol) and 2-(5-(methoxycarbonyl)thiophen-2-yl)acetic acid 18, (260 mg,1.30 mmol) in CH₂Cl₂ (5 mL). The reaction mixture was stirred overnightat room temperature in argon atmosphere. After completion of reactionthe reaction mixture was diluted with mixed solvent (CHCl₃:i-PrOH=4:1,10 mL) and washed with sat. NH₄Cl. The organic layer was dried(anhydrous sodium sulfate) and concentrated in vacuo. The crude productwas chromatographed on silica gel (Hexanes/EtOAc, 7:1) to yield titlecompound 21. (378 mg, 67%). ¹H NMR (CHCl₃, 400 MHz): δ 7.91 (d, J=8.2,Hz, 2H), 7.61 (d, J=3.6, 1H), 7.38 (m, 3H), 7.15 (m, 2H), 3.91 (s, 3H),3.80 (m, 4H), 3.50 (s, 2H), 0.85 (s, 9H), 0.02 (s, 6H); ¹³C NMR (CHCl₃,100 MHz): δ 170.2, 167.0, 145.1, 131.5, 129.5, 129.1, 128.6, 128.5,127.5, 127.0, 60.1, 52.1, 52.0, 41.4, 25.8, 18.2, −5.4; [M+H]⁺=434.84(APCI+).

5-(2-((2-((tert-butyldimethylsilyl)oxy) ethyl)(phenyl)amino)-2-oxoethyl)-N-hydroxythiophene-2-carboxamide (22)

Hydroxylamine (0.5 mL, 50% water solution) was added to a solutioncontaining methyl 5-(2-((2-((tert-butyldimethylsilyl)oxy)ethyl)(phenyl)amino)-2-oxoethyl)thiophene-2-carboxylate) 21, (250 mg, 0.576mmol) in THF/MeOH (1:1, 2 mL). Reaction mixture was treated withcatalytic amount of KCN (˜0.5 mg) and stirred at room temperature inargon atmosphere for 16 h. Then solution was acidified by NH₄Cl/HClsolution to pH ˜4. The mixture was diluted with mixed solvent(CHCl₃:i-ProH=4:1, 10 mL) and washed with sat. NH₄Cl. The organic layerwas dried (anhydrous sodium sulfate) and concentrated in vacuo. Thecrude product was purified on silica gel chromatography (CH₂Cl₂/MeOH,10:1) to yield the target compound 22 (165 mg, 66%). ¹H NMR (CD₃OD, 400MHz): δ 7.64 (d, J=8.4 Hz, 2H), 7.61 (d, J=3.6, 1H), 7.38 (m, 3H), 7.15(m, 2H), 3.80 (m, 4H), 3.54 (s, 2H), 0.88 (s, 9H), 0.05 (s, 6H); ¹³C NMR(CD₃OD, 100 MHz): δ 171.0, 167.0, 142.6, 139.7, 130.8, 129.7, 128.8,128.4, 127.6, 126.2, 60.7, 52.0, 41.0, 26.2, 18.0, −5.2; [M+H]⁺=435.65(APCI+).

N-hydroxy-5-(2-((2-hydroxyethyl)(phenyl)amino)-2-oxoethyl)thiophene-2-carboxamide (23)

Thiophene 22 (75 mg, 0.172 mmol) was dissolved in 2% HCl in MeOH (5 mL)and stirred for 3 h. Then the reaction mixture was concentrated invacuo. The crude product was purified by preparative chromatography onsilica gel (CH₂Cl₂/MeOH, 15:1) to yield target compound 23. (45 mg,81%). ¹H NMR (CD₃OD, 400 MHz): δ 7.64 (d, J=8.4 Hz, 2H), 7.61 (d, J=3.6,1H), 7.38 (m, 3H), 7.15 (m, 2H), 3.86 (t, J=6.0 Hz, 2H), 3.68 (t, J=6.0Hz, 2H), 3.55 (s, 2H); ¹³C NMR (CD₃OD, 100 MHz): δ 172.0, 166.9, 142.7,139.7, 130.9, 129.9, 129.4, 128.7, 128.5, 127.1, 58.8, 51.8, 41.0;[M+1H]⁺=321.3 (APCI+).

Example 4. Synthesis of Compound 32

HDAC inhibitor 32 was prepared according to the protocols shown inSchemes 6 and 7. Amine 29 was coupled to acid 27 to form amide 30. Themethyl ester of 30 was converted directly, using aqueous hydroxylamine,to the corresponding hydroxamic acid, which was deprotected with 2%aqueous HCl to afford compound 32.

Reagents and conditions: a) NaCN, MeOH/H₂O, 70° C., 5 h; b) aq NaOH(6N), MeOH, 90° C. 12 h; c) MeOH/cat. H₂SO₄ 90° C. 18 h; d) MeOH, H₂O,K₂CO₃, rt, 12 h.

Methyl 4-(cyanomethyl)benzoate (24)

Commercially available 4-bromomethylbenzoic acid methyl ester (5.0 g)was dissolved in methanol (40 mL). A potassium cyanide solution (5.63 gin 8 mL water) was added dropwise over 15 min. The resulting suspensionwas heated to reflux for 5 h. Volatiles were removed under reducedpressure and the residue dissolved in diethylether and water. Theorganic layer was concentrated to a dark oil which was purified bycolumn chromatography (5% ethyl acetate in hexane) to give theintermediate. Yield 3.82 g, 58.6%. [M+H]⁺=176.3 (APCI+). ¹H NMR (CHCl₃,400 MHz): δ 8.05 (d, J=8.1 Hz, 1H), 7.42 (d, J=8.1, 1H), 3.93 (s, 3H),3.81 (s, 2H).

4-(carboxymethyl)benzoic acid (25)

A solution of methyl 4-(cyanomethyl)benzoate 24, (2.0 g, 11.4 mmol) in6M Sodium hydroxide (15 mL) and methanol (15 mL) was heated at 90° C.overnight. After concentrating the reaction mixture, the aqueous layerwas washed with dichloromethane (30 mL×2), then acidified to pH-3 with12M HCl. The aqueous solution was extracted with ethyl acetate (20mL×2). Organics was combined, dried over Na₂SO₄ and evaporated in vacuoto give titled compound. (1.45 mg, 70%). [M+H]⁺=181.4 (APCI+).

Methyl 4-(2-methoxy-2-oxoethyl)benzoate (26)

A solution of 4-(carboxymethyl)benzoic acid 25, (1.00 g, 5.55 mmol) andH₂SO₄ (2 mL) in methanol (20 mL) was heated at 90° C. overnight. Afterconcentrating the reaction mixture, the crude was taken into EtOAc (30mL) and washed with sat. NaHCO₃ (30 mL). Then the organic layer wasdried over Na₂SO₄ and evaporated in vacuo. Crude material was purifiedon silica gel column (EtOAc:Hexanes=1:6) to give the title compound 26.(1.05 mg, 91%). ¹H NMR (CHCl₃, 400 MHz): δ 8.00 (d, J=8.1 Hz, 1H), 7.37(d, J=8.1, 1H), 3.90 (s, 3H), 3.69 (s, 3H), 3.67 (s, 2H); ¹³C NMR(CHCl₃, 100 MHz): δ 167.7, 138.8, 129.8, 129.3, 128.9, 52.5, 52.3, 41.2;[M+H]⁺=209.3 (APCI+).

2-(4-(methoxycarbonyl)phenyl) acetic acid (27)

A solution of methyl 4-(2-methoxy-2-oxoethyl)benzoate 26, (800 mg, 3.85mmol) and K₂CO₃ (929 mg, 5.67 mmol) in water/methanol mixture (20 mL,1:1) was stirred at room temperature 4 hrs. After concentrating thereaction mixture to 5 mL diluted with water (20 mL). Then the aqueouslayer was washed with dichloromethane (20 mL×2), and acidified to pH-3with 12M HCl. The aqueous solution was extracted with ethyl acetate (20mL×2). Organics was combined, dried over Na₂SO₄ and evaporated in vacuoto give titled compound 27. (620 mg, 83%). ¹H NMR (CHCl₃, 400 MHz): δ7.90 (d, J=8.1 Hz, 1H), 7.42 (d, J=8.1, 1H), 3.85 (s, 3H), 3.68 (s, 2H);[M+H]³⁰=195.4 (APCI+).

Reagents and conditions: a) Imidazole, TBSCl, CH₂Cl₂, 0° C.-rt; b) 29,EDCI, Et₃N, CH₂Cl₂, rt, 18 h; c) 50% (w/w) aq. NH₂OH, MeOH, rt; d) 2%aq. HCl, MeOH, 0° C.-rt.

N-benzyl-2-((tert-butyldimethylsilyl)oxy)ethan-1-amine (29)

TBDMS-Cl (1.28 g, 8.02 mmol) and imidazole (1.45 g, 21.86 mmol) wasadded to a solution containing 2-(benzylamino)ethan-1-ol 1, (1.10 g,7.29 mmol) in CH₂Cl₂ (10 mL). The reaction mixture was stirred at roomtemperature in argon atmosphere for 3 h. Then the reaction was quenchedwith sat. NH₄Cl. and washed with water (10 mL×2) and brine (10 mL×2).The organic layer was dried (anhydrous sodium sulfate) and concentratedin vacuo. The crude product was chromatographed on silica gel(Hexanes/EtOAc, 7:1) to yield target compound 29. Yield 1.59 g, 82%.[M+H]⁺=266.26 (APCI+).

Methyl 4-(2-(benzyl(2-((tert-butyldimethylsilyl)oxy) ethyl)amino)-2-oxoethyl)benzoate (30)

EDCI (582.0 mg, 3.4 mmol) was added to a solution containingN-benzyl-2-((tert-butyldimethylsilyl)oxy)ethan-1-amine 29, (848 mg, 3.2mmol) and 2-(4-(methoxycarbonyl)phenyl)acetic acid 27, (504 mg, 2.6mmol) in CH₂Cl₂ (5 mL). The reaction mixture was stirred overnight atroom temperature in argon atmosphere. After completion of reaction thereaction mixture was diluted with mixed solvent (CHCl₃:i-PrOH=4:1, 10mL) and washed with sat. NH₄Cl. The organic layer was dried (anhydroussodium sulfate) and concentrated in vacuo. The crude product waschromatographed on silica gel (Hexanes/EtOAc, 7:1) to yield titlecompound 30. (820 mg, 58%). ¹H NMR (CHCl₃, 400 MHz): δ 7.6 (d, J=8.1,Hz, 2H), 7.32 (m, 3H), 7.15 (m, 4H), 4.90 (s, 2H), 3.91 (s, 3H), 3.80(m, 4H), 3.50 (s, 2H), 0.85 (s, 9H), 0.02 (s, 6H); [M+H]⁺=442.4 (APCI+).

4-(2-(benzyl(2-((tert-butyldimethylsilyl)oxy)ethyl)amino)-2-oxoethyl)-N-hydroxy-benzamide(31)

Hydroxylamine (0.5 mL, 50% water solution) was added to a solutioncontaining methyl methyl4-(2-(benzyl(2-((tert-butyldimethylsilyl)oxy)ethyl)amino)-2-oxoethyl)benzoate30, (250 mg, 0.576 mmol) in THF/MeOH (1:1, 2 mL). Reaction mixture wastreated with cat. amount of KCN (˜0.5 mg) and stirred at roomtemperature in argon atmosphere for 16 h. Then solution was acidified byNH₄Cl/HCl solution to pH ˜4. The mixture was diluted with mixed solvent(CHCl₃:i-PrOH=4:1, 10 mL) and washed with sat. NH₄Cl. The organic layerwas dried (anhydrous sodium sulfate) and concentrated in vacuo. Thecrude product was purified on silica gel chromatography (CH₂Cl₂/MeOH,15:1) to yield the target compound 31 (130 mg, 52%). ¹H NMR (CD₃OD, 400MHz): δ 7.68 (d, J=8.4 Hz, 2H), 7.55 (m, 3H), 7.10 (d, J=8.0 Hz, 2H),6.92 (d, J=8.0 Hz, 2H), 4.85 (s, 2H), 3.80 (m, 4H), 3.54 (s, 2H), 0.88(s, 9H), 0.05 (s, 6H); [M+H]⁺=443.65 (APCI+).

4-(2-(benzyl(2-hydroxyethyl)amino)-2-oxoethyl)-N-hydroxy-benzamide (32)

4-(2-(benzyl(2-((tert-butyldimethylsilyl)oxy)ethyl)amino)-2-oxoethyl)-N-hydroxybenzamide, 31 (100 mg, 0.226 mmol) wasdissolved in 2% HCl in MeOH (5 mL) and stirred for 3 h. Then thereaction mixture was concentrated in vacuo. The crude product waspurified by preparative chromatography on silica gel (CH₂Cl₂/MeOH, 10:1)to yield target compound 32. (38 mg, 51%). ¹H NMR (CD₃OD, 400 MHz): δ7.64 (d, J=8.4 Hz, 2H), 7.45 (m, 3H), 7.29 (d, J=8.0 Hz, 2H), 7.14 (d,J=8.0 Hz, 2H), 3.86 (t, J=6.0 Hz, 2H), 3.68 (t, J=6.0 Hz, 2H), 3.55 (s,2H); ¹³C NMR (CD₃OD, 100 MHz): δ 173.0, 167.9, 141.8, 139.2, 130.9,129.9, 129.4, 128.7, 128.5, 127.1, 58.8, 51.8, 49.6, 41.0; [M+H]⁺;[M+H]⁺=329.3 (APCI+).

Example 5. Synthesis of Compound 36

HDAC inhibitor 36 was accessed according to the protocols shown inScheme 8. Acid 33 was coupled to 4-(carboxymethyl)benzoic acid to formester 34. The acid of compound 34 was coupled to 0-protectedhydroxylamine to form protected hydroxamate 35. Deprotection underacidic conditions gave inhibitor 36.

Reagents and conditions: a) Boc₂O, CH₂Cl₂, 0° C.-rt, 5 h; b)4-(carboxymethyl)benzoic acid, EDCI, Et₃N, CH₂Cl₂, rt, 18 h; c) NH₂OTBS,EDCI, Et₃N, CH₂Cl₂, rt, 18 h; d) 2% aq. HCl, MeOH, 0° C.-rt.

tert-butyl (2-hydroxyethyl)(phenyl)carbamate (33)

2-Phenylamino-ethanol, 10 (2.5 g, 18 mmol) and di-t-butyl-dicarbonate(0.8 g, 1.5 eq.) in 25 mL of THF was heated to 55° C. for 7 h. Volatilewas then removed in vacuo. The crude product was recrystallized fromCH₂Cl₂ and hexane to give white crystalline material 33. (4 g, 65%). ¹HNMR (CHCl₃, 400 MHz): δ 7.66 (d, J=8.0, 2H), 7.30 (m, 3H), 3.80 (s, 2H),1.4 (s, 9H), 3.89 (s, 3H); [M+H]⁺=238.4 (APCI+).

4-(2-(2-((tert-butoxycarbonyl)(phenyl)amino) ethoxy)-2-oxoethyl) benzoicacid (34)

EDCI (407.0 mg, 2.8 mmol) was added to a solution containing tert-butyl(2-hydroxyethyl)(phenyl)carbamate 33, (660 mg, 2.8 mmol) and4-(carboxymethyl)benzoic acid (468 mg, 2.6 mmol) in CH₂Cl₂ (5 mL). Thereaction mixture was stirred for 5 hrs at room temperature in argonatmosphere. After completion of reaction the reaction mixture wasdiluted with with sat. NH₄Cl and extracted with EtOAc (30 mL×3). Theorganic layer was dried (anhydrous sodium sulfate) and concentrated invacuo. The crude product was chromatographed on silica gel(Hexanes/EtOAc, 7:1) to yield title compound 34. (610 mg, 60%).[M+H]⁺=400.2 (APCI+).

2-((tert-butoxycarbonyl)(phenyl)amino)ethyl-2-(4-(((tert-butyl-dimethylsilyl)oxy)carbamoyl)phenyl) acetate (35)

EDCI (203 mg, 1.4 mmol) was added to a solution containingO-(tert-butyl-dimethylsilyl) hydroxylamine, (162 mg, 1.1 mmol) in CH₂Cl₂(5 mL). The reaction mixture was stirred for 18 hrs at room temperaturein argon atmosphere. After completion of reaction the reaction mixturewas diluted with with sat. NH₄Cl and extracted with EtOAc (30 mL×3). Theorganic layer was dried (anhydrous sodium sulfate) and concentrated invacuo. The crude product was chromatographed on silica gel(Hexanes/EtOAc, 7:1) to yield title compound 35. (275 mg, 47%).[M+H]⁺=529.5 (APCI+).

2-(phenylamino)ethyl 2-(4-(hydroxycarbamoyl)phenyl) acetate (36)

2-((tert-butoxycarbonyl)(phenyl)amino)ethyl2-(4-(((tert-butyl-dimethylsilyl)oxy)carbamoyl) phenyl) acetate 35 (100mg, 0.189 mmol) was dissolved in 2% HCl in MeOH (5 mL) and stirred for 3h. Then the reaction mixture was concentrated in vacuo. The crudeproduct was purified by preparative chromatography on silica gel(CH₂Cl₂/MeOH, 10:1) to yield target compound 36. (28 mg, 47%). ¹H NMR(CD₃OD, 400 MHz): δ 7.71 (d, J=8.4 Hz, 2H), 7.38 (d, J=8.4 Hz, 2H), 7.12(t, J=8.0, Hz 3H), 6.65 (m, 3H), 4.27 (t, J=6.0 Hz, 2H), 3.73 (s, 2H),3.39 (t, J=6.0 Hz, 2H); ¹³C NMR (CD₃OD, 100 MHz): δ 171.5, 166.5, 148.3,138.2, 130.9, 129.3, 129.4, 128.7, 126.9, 116.9, 112, 7, 63.5, 42.1,40.2; [M+H]⁺ 314.38 (APCI+).

Example 6: Cell Assay of Compounds 8 and 11

As shown in the cell based (LNCaP-human prostate) assay (FIG. 2),compounds 8 and 11 caused the accumulation of acetylated α-tubulin, asubstrate of HDAC6. However, compounds 8 and 11 did not causeaccumulation of actylated histones, which is not a substrate of HDAC6,indicating HDAC6 selectivity.

Example 7: HDAC6 vs. HDAC1 Activity

Compounds 8 and 11 were assayed for inhibition of recombinant HDAC6 andHDAC1 (Table 1). Compound 8 has an IC₅₀ inhibitory activity for HDAC6 of31 nM compared with 1128 nM for HDAC1 (ratio HDAC1:HDAC6=36.38).Compound 11 has an IC₅₀ inhibitory activity for HDAC6 of 11 nM comparedwith 270 nM for HDAC1 (ratio HDAC1:HDAC6=24.54).

Compound 8 is one hundred fold more potent inhibitor of HDAC6 than SAHA(suberoylanilide hydroxamic acid). Compound 8 is assayed against elevenzinc containing HDACS and is 15 to almost 400 fold more potent inhibitorof HDAC6 than other zinc dependent HDAC's.

TABLE 1 Ratio: HDAC1/ Compound IC₅₀ (nM) HCAC1 IC₅₀ (nM) HCAC6 HDAC6  81128 31 36.38 11 270 11 24.54 SAHA 54 21 3.09 Tubacin 193 45 4.3

Example 8. Cell Growth Vs. Cell Viability

The effect of compound 8 on the cell growth and viability of normal(HFS, human foreskin fibroblast) and transformed (LNCaP, human prostateadenocarcinoma) cells cultured with 8, 16, 32 or 64 μM HPB for up to 72h was evaluated. Compound 8 inhibited cell growth of normal andtransformed cells in a concentration dependent manner (FIG. 3), but didnot induce cell death of normal or transformed cells (FIG. 4).

Example 9. Acetylation of Alpha-Tubulin Vs. Histones

In normal (HFS) and transformed (LNCAP) cells, compound 8, at 8 μM to 64μM, caused accumulation of acetylated alpha-tubulin, a substrate ofHDAC6 (Kovacs J J, et al. 2005; Parmigiani R B, et al. 2008), but not ofacetylated histones (FIG. 5). SAHA induced the accumulation ofacetylated alpha-tubulin and histone H3 (Marks, P. et al. 2007; Lee etal. 2010; Namdar et al. 2010).

Example 10. Mouse Toxicity Studies

Toxicity of compound 8 in mice was determined. Compound 8 is welltolerated in animals. Mice were intraperitoneally injected daily for 5days with 100, 200, or 300 mg/kg compound 8. There was no weight loss inthe mice (FIG. 6). The effects of compound 8 on the acetylation ofalpha-tubulin and histones in the spleen isolated from mice treated withcompound 8 were analyzed at three time points after the administrationof the drug. At 1.5 h after injection of compound 8, an increasedaccumulation of acetylated tubulin was found in the spleen (FIG. 7). By5 h after injection of compound 8, the accumulation of acetylatedtubulin was reduced to the level seen in vehicle-treated controls. Therewas no detectable accumulation of acetylated histones in the spleen fromthe mice receiving the compound (FIG. 7).

Example 11. Combination of Compound 8 with Anti-Cancer Agents

It has been reported that inhibition of HDAC6 by either si-RNA ortubacin potentiates the cytotoxicity of anti-cancer drugs in transformedbut not normal cells (Namdar et al. 2010; Lee et al. 2013). To assesswhether selective inhibition of HDAC6 by compound 8 enhances cell deathof normal and transformed cells in culture with anticancer agents, cellsare cultured with compound 8 and the topoisomerase II inhibitor,etoposide, or the mitotic inhibitor, paclitaxel, or the pan-HDACinhibitor, SAHA, for 72 h.

In HFS (normal) cells, compound 8 alone or in combination withetoposide, paclitaxel, or SAHA inhibits cell growth but does not induceloss of cell viability.

LNCaP (transformed) cells cultured with 50 μM etoposide and 16 μMcompound 8 demonstrates inhibition in cell growth and loss of cellviability to a greater extent than LNCaP cells cultured with etoposidealone. LNCaP cell death is enhanced in cultures with compound 8 and 5 μMSAHA compared with cultures with SAHA alone. Combined treatment withpaclitaxel and compound 8 caused increases cell death in LNCaP cellscompared to either drug alone.

Example 12. Mouse Studies with Combination of Compound 8 withAnti-Cancer Drugs

The effects of compound 8 in combination with the anti-cancer drug,etoposide, are examined in nude mice implanted with theandrogen-dependent CWR22 human prostate cancer xenograft, which wasgrown subcutaneously. Daily administration of either 300 mg/kg compound8 or weekly administration of 3 mg/kg etoposide alone for 21 days causesno significant suppression of the growth of established CWR22 tumors andno weight loss. Daily administration of compound 8 and weeklyadministration of etoposide causes suppression of the growth ofestablished CWR22 tumors, such that doses cause reductions in the meanfinal tumor volume compared with vehicle-treated control animals. Tumorsand spleen are removed from the animals, and histones and proteins areextracted for the detection of acetylated lysine patterns. There isincreased accumulation of acetylated alpha-tubulin in CWR22 tumors andspleen from mice treated with compound 8, etoposide, or combination ofcompound 8 and etoposide (FIG. 6D). Increased levels of accumulation ofhistones are found in tumors of mice injected with etoposide orcombination of etoposide and compound 8, but not with compound 8 alone.This data indicates that compound 8 is a selective inhibitor of HDAC6 invivo and enhances anti-tumor effect of a chemotherapeutic agent.

Example 13. Additional Selective HDAC6 Inhibitors

The compounds of the present invention are HDAC6 selective inhibitors.An additional aspect of the invention provides synthetic methods andchemical intermediates that may be used to synthesize additional HDAC6inhibitors. Additional compounds, which are synthesized according tomethods similar to those described in Schemes 1-8 or according tomethods known in the art, have analogous activity to compounds 8 and/or11. The left hand portion of the compound (R₁) is also varied to improvesolubility and drug-like properties and compounds with various R₁ groupsfunction analogously to compounds 8 and/or 11.

Example 14. Administration of Compound 8 or 11

An amount of compound 8 or 11 is administered to a subject afflictedwith a neurodegenerative disease, cancer, or HIV infection. The amountof the compound is effective to treat the subject.

An amount of compound 8 or 11 in combination with an anti-cancer agentis administered to a subject afflicted with cancer. The amount of thecompound is effective to enhance the anti-cancer activity of theanti-cancer agent.

An amount of compound 8 or 11 in combination with etoposide, paclitaxel,or SAHA, is administered to a subject afflicted with cancer. The amountof the compound is effective to enhance the anti-cancer activity of theetoposide, paclitaxel, or SAHA.

An amount of an analogue of compound 8 or 11 is administered to asubject afflicted with a neurodegenerative disease, cancer, or HIVinfection. The amount of the analogue is effective to treat the subject.

An amount of an analogue of compound 8 or 11, in combination with ananti-cancer agent is administered to a subject afflicted with cancer.The amount of the analogue is effective to enhance the anti-canceractivity of the anti-cancer agent.

An amount of an analogue of compound 8 or 11 in combination withetoposide, paclitaxel, or SAHA is administered to a subject afflictedwith cancer. The amount of the analogue is effective to enhance theanti-cancer activity of the etoposide, paclitaxel, or SAHA.

DISCUSSION

There are eleven zinc dependent histone deacetylase (HDAC) in humans.All HDAC's are nuclear proteins except for HDAC6. HDAC6 is unique amongHDACs in being a cytoplasmic protein with two catalytic sites and anubiquitin binding site. HDAC6 substrates include a number of proteins,eg. tubulin, peroxidases, certain DNA repair proteins, but not histones.HDAC6 has a role in the cellular response to accumulation of misfoldedand aggregated proteins which are catalysts of certain neurologicaldisconects such as Alzheimer's, Parkinson's, and Huntington's diseases.

HDAC6-selective inhibitors were identified on the basis of accumulationof acetylated tubulin without accumulation of acetylated histones.Compound 8 and 11 were identified as HDAC6-selective inhibitors. As showin FIG. 2, significant levels of tubulin acylation were present withoutinduction of H3 acetylation.

As indicated by the cell based (LNCaP-human prostate) assays, compounds8 inhibited cell number but does not decrease cell viability. UnlikeSAHA, which kills LNCaP cells, there is no detectable death of LNCaPcells with compound 8 even at concentrations as high as 32 μM.

Compound 8 inhibited HDAC6 in vitro with approximately 36-foldselectivity against HDAC6 over HDAC1 enzyme. Concentrations as high as16 μM of compound 8 selectively induced accumulation of acetylatedalpha-tubulin and acetylated PRX, substrates of HDAC6, but not ofacetylated histones in both normal and transformed cells. Histones arenot a substrate of HDAC6. Compound 8 in concentrations ≤16 μM do notinduce normal cell death.

Culture of transformed cells with compound 8 enhances the cytotoxicityof anti-cancer drugs through increased induction of apoptosis andaccumulation of DNA damage. Compound 8 also enhances etoposide orSAHA-induced transformed cell death. Compound 8 in combination withetoposide significantly enhances the anti-tumor effect of etoposide innude mice with androgen-dependent CWR22 human prostate cancer xenograft.

These findings indicate that selective inhibition of HDAC6 incombination with anti-cancer drugs may be an important avenue to enhancetherapeutic efficacy of such drugs in treating human cancers.

REFERENCES

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What is claimed is:
 1. A compound having the structure:

wherein R₁ is halogen, —NR₅R₆, —NR₅—C(═O)—R₆, —NH—C(═O)—OR₇, —OR₇, —NO₂,—CN, —SR₇, —SO₂R₇, —CO₂R₇, CF₃, —SOR₇, —POR₇, —C(═S)R₇, —C(═O)—NR₅R₆,—CH₂—C(═O)—NR₅R₆, —C(═NR₅)R₆, —P(═O)(OR₅)(OR₆), —P(OR₅)(OR₆), —C(═S)R₇,C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, aryl, heteroaryl, orheterocyclyl, wherein R₅, R₆, and R₇ and are each, independently, H,C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl, hydroxyalkyl,cycloalkyl, heterocycloalkyl, aryl, heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅alkyl-NH-aryl; Ar₁ is phenyl or thiophene; wherein when Ar₁ is phenyl,then R₁ is other than —C(═O)—NR₅R₆, where one of R₅ or R₆ is phenyl orquinoline and the other of R₅ or R₆ is —CH₂CH₂OH, or where one of R₅ orR₆ is quinoline and the other of R₅ or R₆ is H; and wherein when Ar₁ isphenyl, then R₁ is other than —NR₅—C(═O)—R₆, where R₅ is H and R₆ isquinoline, or a pharmaceutically acceptable salt thereof.
 2. Thecompound of claim 1, wherein Ar₁ is


3. The compound of claim 1, wherein R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆,or —CO₂R₇, wherein R₅, R₆, and R₇ and are each, independently, H, C₁₋₅alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl, hydroxyalkyl,cycloalkyl, heterocycloalkyl, aryl, heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅alkyl-NH-aryl.
 4. The compound of claim 3, wherein R₁ is —C(═O)—NR₅R₆,—NR₅—C(═O)—R₆, or —CO₂R₁, wherein R₅, R₆, and R₇ and are each,independently, H, C₁₋₅ alkyl, hydroxyalkyl, aryl, heteroaryl, C₁₋₅alkyl-aryl, or C₁₋₅ alkyl-NH-aryl.
 5. The compound of claim 4, whereinR₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇, wherein R₅ is C₁₋₅ alkyl,hydroxyalkyl, aryl or heteroaryl; R₆ is C₁₋₅ alkyl, hydroxyalkyl, arylor heteroaryl; and R₇ is C₁₋₅ alkyl, hydroxyalkyl, aryl, heteroaryl, orC₁₋₅ alkyl-NH-aryl.
 6. The compound of claim 4, wherein R₁ is—C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇, wherein R₅, R₆, and R₇ and areeach, independently, phenyl, —CH₂CH₂OH, —CH₂-phenyl, or—CH₂CH₂N(H)-phenyl.
 7. The compound of claim 6, wherein R₁ is—C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or —CO₂R₇, wherein R₅, R₆, and R₇ and areeach, independently,

R₁ is —C(═O)—NR₅R₆, wherein R₅ is

or R₁ is —NR₅—C(═O)—R₆, wherein R₅ is

or R₁ is —CO₂R₇, wherein R₇


8. The compound of claim 1 having the structure:

wherein R₁ is halogen, —NR₅R₆, —NR₅—C(═O)—R₆, —NH—C(═O)—OR₇, —OR₇, —NO₂,—CN, —SR₇, —SO₂R₇, —CO₂R₇, CF₃, —SOR₇, —POR₇, —C(═S)R₇, —C(═O)—NR₅R₆,—CH₂—C(═O)—NR₅R₆, —C(═NR₅)R₆, —P(═O)(OR₅)(OR₆), —P(OR₅)(OR₆), —C(═S)R₇,C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, aryl, heteroaryl, orheterocyclyl, wherein R₅, R₆, and R₇ and are each, independently, H,C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl, hydroxyalkyl,cycloalkyl, heterocycloalkyl, aryl, heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅alkyl-NH-aryl; wherein R₁ is other than —C(═O)—NR₅R₆, where one of R₅ orR₆ is phenyl or quinoline and the other of R₅ or R₆ is —CH₂CH₂OH, orwhere one of R₅ or R₆ is quinoline and the other of R₅ or R₆ is H; andwherein R₁ is other than —NR₅—C(═O)—R₆, where R₅ is H and R₆ isquinoline, or a pharmaceutically acceptable salt thereof.
 9. Thecompound of claim 1 having the structure:

wherein R₁ is halogen, —NR₅R₆, —NR₅—C(═O)—R₆, —NH—C(═O)—OR₇, —OR₇, —NO₂,—CN, —SR₇, —SO₂R₇, —CO₂R₇, CF₃, —SOR₇, —POR₇, —C(═S)R₇, —C(═O)—NR₅R₆,—CH₂—C(═O)—NR₅R₆, —C(═NR₅)R₆, —P(═O)(OR₅)(OR₅), —P(OR₅)(OR₆), —C(═S)R₇,C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, aryl, heteroaryl, orheterocyclyl, wherein R₅, R₆, and R₇ and are each, independently, H,C₁₋₅ alkyl, C₂₋₅ alkenyl, C₂₋₅ alkynyl, heteroalkyl, hydroxyalkyl,cycloalkyl, heterocycloalkyl, aryl, heteroaryl, C₁₋₅ alkyl-aryl, or C₁₋₅alkyl-NH-aryl, or a pharmaceutically acceptable salt thereof.
 10. Thecompound of claim 1, wherein R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or—CO₂R₇, wherein R₅ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl; R₆is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl; and R₇ is C₁₋₅ alkyl,hydroxyalkyl, aryl, heteroaryl, or C₁₋₅ alkyl-NH-aryl; and Ar₁ is phenylor thiophene, or a pharmaceutically acceptable salt thereof.
 11. Thecompound of claim 1, wherein R₁ is —C(═O)—NR₅R₆, —NR₅—C(═O)—R₆, or—CO₂R₇, wherein R₅ is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl; R₆is C₁₋₅ alkyl, hydroxyalkyl, aryl or heteroaryl; and R₇ is C₁₋₅ alkyl,hydroxyalkyl, aryl, heteroaryl, or C₁₋₅ alkyl-NH-aryl; and Ar₁ is

or a pharmaceutically acceptable salt thereof.
 12. The compound of claim8 having the structure:

or a pharmaceutically acceptable salt thereof.
 13. The compound of claim9 having the structure:

or a pharmaceutically acceptable salt thereof.
 14. A pharmaceuticalcomposition comprising the compound of any one of claims 1-13 and apharmaceutically acceptable carrier.
 15. A method of inhibiting theactivity of a histone deacetylase in a cell comprising contacting thehistone deacetylase with the compound of any one of claims 1-13 so as toinhibit the activity of the histone deacetylase.
 16. The method of claim15, wherein the histone deacetylase is HDAC6.
 17. A method of treating aneurodegenerative disease in a subject comprising administering aneffective amount of the compound of any one of claims 1-13 to thesubject so as to treat the neurodegenerative disease in the subject. 18.The method of claim 17, wherein the neurodegenerative disease isParkinson's disease, Alzheimer's disease, Huntington's disease orNiemann-Pick type C disease.
 19. A method of treating a diseaseassociated with defective lipid transport in a subject comprisingadministering an effective amount of the compound of any one of claims1-13 to the subject so as to treat the disease in the subject.
 20. Themethod of claim 19, wherein the disease associated with defective lipidtransport is Stargardt disease, macular degeneration, Harlequinichthyosis or Tangier disease.
 21. A method of treating cancer in asubject comprising administering an effective amount of the compound ofany one of claims 1-13 to the subject so as to treat the cancer in thesubject.
 22. A method of treating HIV infection or latent HIV infectionin a subject comprising administering an effective amount of thecompound of any one of claims 1-13 to the subject so as to treat the HIVinfection or the latent HIV infection in the subject.
 23. A method oftreating a subject afflicted with cancer comprising periodicallyadministering to the subject a) an amount of the compound of any one ofclaims 1-13 or a pharmaceutically acceptable salt thereof, and b) ananti-cancer agent, wherein the amounts when taken together are moreeffective to treat the subject than when each agent at the same amountis administered alone.
 24. The method of claim 23, wherein theanti-cancer agent is selected from x-radiation, ionizing radiation, aDNA damaging agent, a DNA intercalating agent, a microtubule stabilizingagent, a microtubule destabilizing agent, a spindle toxin, abarelix,aldesleukin, alemtuzumab, alitertinoin, allopurinol, altretamine,amifostin, anakinra, anastrozole, arsenic trioxide, asparaginase,azacitidine, bevacizumab, bexarotene, bleomycin, bortezomib, busulfan,calusterone, capecitabine, carboplatin, carmustine, celecoxib,cetuximab, chlorambucil, cisplatin, cladribine, clofarabine,cyclophosphamide, cytarabine, dacarbazine, dactinomycin, actinomycin D,dalteparin sodium, darbepoetin alfa, dasatinib, daunorubicin,daunomycin, decitabine, denileukin, dexrazoxane, docetaxel, doxorubicin,dromostanolone propionate, exulizumab, epirubicin, epoetin alfa,erlotinib, estramustine, etoposide phosphate, etoposide, VP-16,exemestane, fentanyl citrate, filgrastim, floxuridine, fludarabine,fluorouracil, fulvestrant, gefitinib, gemcitabine, gosereline acetate,histrelin acetate, hydroxyurea, ibritumomab tiuxetan, idarubicin,ifosfamide, imatinib mesylate, interferon alfa 2a, interferon alfa 2b,irinotecan, lapatinib ditosylate, lenalidomide, letrozole, leucovrin,leuprolide acetate, levamisole, lomustine, meclorethamine, megestrolacetate, melphalan, mercaptopurine, mesna, methotrexate, methoxsalen,mitomycin C, mitotane, mitoxantrone, nandrolone phenpropionate,nelarabine, nofetumomab, oprelvekin, oxaliplatin, paclitaxel,palifermin, pamidronate, panitumumab, pegademase, pegaspargase,pegfilgrastim, peginterferon alfa 2b, pemetrexed disodium, pentostatin,pipobroman, plicamycin, mithramycin, porfimer sodium, procarbazine,quinacrine, rasburicase, rituximab, SAHA, sargrmostim, sorafenib,streptozocin, sunitinib, sunitinib maleate, talc, tamoxifen,temozolomide, teniposide, VM-26, testolactone, thalidomide, thioguanine,G-TG, thiotepa, topotecan, toremifene, tositumomab, trastuzumab,tretinoin ATRA, uracil mustard, valrunicin, vinblastine, vincristine,vinorelbine, vorinostat, zoledronate, zoledronic acid, abraxane orbrentuximab vedotin.